How to Mark Revisions in a Clean Manuscript
By Dr. Zubair Khalid, DVM, MS, PhD ·
Quick Answer
- Submit a clean manuscript with no visible track changes, and provide a separate marked-up version so editors and reviewers can verify each revision.
- Write a response letter that lists every change point by point, using page and line numbers from the clean version for easy cross-reference.
- Keep the marked-up file and response letter as permanent records, since journals may request them during ethics or reproducibility checks.
At a Glance
| Document | Purpose | When to Use | Key Limitation |
|---|---|---|---|
| Clean manuscript | Final version for publication | Submit as the primary file | Does not show what changed |
| Marked-up manuscript | Shows every revision to editors and reviewers | Submit as a supplementary file | Must match the clean version exactly |
| Response letter | Explains each change and the reason behind it | Submit with the clean manuscript | Requires careful numbering and cross-referencing |
| Original submitted version | Baseline for comparison | Keep in your records | Needed if a dispute arises about what was changed |
Understanding the Clean Manuscript Requirement
Journals and funding agencies expect authors to submit a manuscript that reads as a finished document. A file with visible track changes, colored text, or margin comments is not a clean manuscript. The National Library of Medicine hosts research-method references that describe how manuscripts move through preparation, peer review, and revision, and the consistent expectation is that the final submitted file is readable without editing marks.
The clean manuscript serves a practical purpose. Editors, copy editors, and typesetters work from the submitted file. If the file contains tracked changes, the production process can become confused about which version of a sentence is the intended one. Reviewers also need to read the manuscript as a finished document so they can judge the overall argument, beyond the patches that were added.
The revision process itself is governed by publication ethics. The Committee on Publication Ethics core practices describe how peer review should work, including the expectation that authors respond to reviewer comments in a transparent way. A clean manuscript plus a separate marked-up version is the standard way to meet that expectation without creating confusion.
The Two File System
The most reliable approach is to prepare two separate files from the same revised document.
The first file is the clean manuscript. This file has no track changes, no comments, no colored text, and no revision markers. It is the version you want the journal to publish after copyediting and typesetting.
The second file is the marked-up manuscript. This file shows every change you made in response to the reviewers. You can create it by turning on track changes and making your edits, or by using a comparison tool that shows the differences between your original submission and your revised version.
The marked-up file serves as evidence. Reviewers can see exactly what you changed and where. The clean file serves as the working document. Editors can move it forward without having to accept or reject changes one by one.
The two files must match. If the marked-up file shows a change that is not in the clean file, or if the clean file contains a change that is not in the marked-up file, the editor will notice the discrepancy. That discrepancy can raise questions about the integrity of the revision process.
Creating the Clean Version
Start with your revised manuscript file. If you have been working with track changes on, you need to accept all changes and delete all comments before you save the clean version.
The process is straightforward in most word processors. Open the file, accept all tracked changes, and delete all comments. Then review the document carefully to make sure no revision markers remain. Check the margins for comment bubbles, check the text for colored or underlined passages, and check the document for any hidden text or metadata that might reveal the revision history.
The National Institutes of Health provides guidance on how grant applications are prepared and reviewed, and the same principle applies to manuscript preparation. The document you submit should be the document you want evaluated. If you submit a file with visible revision markers, the reviewer may focus on the process of revision instead of the substance of your work.
After you save the clean version, create the marked-up version. The easiest way is to use the comparison feature in your word processor. This feature compares your original manuscript with your revised manuscript and produces a new file that shows the differences. The comparison file will show insertions, deletions, and formatting changes.
If you do not have the original manuscript file, you can create the marked-up version by turning on track changes and manually reversing your edits. This is more labor intensive and more prone to error, so it is better to keep the original file.
Writing the Response Letter
The response letter is the document that ties everything together. It is where you explain what you changed and why you changed it. The letter should be organized by reviewer comment, not by the order of changes in the manuscript.
Start with a brief summary of the major changes you made. Then address each reviewer comment in order. For each comment, restate the comment in your own words, describe what you changed, and explain why you made that change. If you did not make a change, explain why you believe the original text was correct.
The response letter should reference the clean manuscript by section, paragraph, and line number. This allows the reviewer to find the change without searching through the entire document. If you are using the marked-up file, you can also reference the page number in the marked-up file.
The EQUATOR Network provides reporting guidelines for many types of studies. These guidelines describe what information should be included in a research report. When you revise a manuscript, you should check whether the reporting guideline for your study type requires additional information. If the guideline requires a new section or a new table, you need to add it and describe it in the response letter.
Numbering and Cross Referencing
The response letter and the marked-up manuscript should use the same numbering system. If you number the reviewer comments as R1.1, R1.2, R1.3, and so on, use the same numbers in the marked-up manuscript. You can add a comment in the margin of the marked-up file that says "R1.1" to show where the change was made.
This cross referencing makes the review process faster and more reliable. The reviewer can read the response letter, see that you addressed comment R1.1, and then find the change in the marked-up manuscript without searching.
The clean manuscript should not contain these numbers. The clean manuscript is the final document, and it should not have any revision markers.
Handling Reviewer Comments You Disagree With
You are not required to make every change a reviewer suggests. The Committee on Publication Ethics describes the peer review process as a dialogue between authors and reviewers. You can disagree with a reviewer, but you must explain why you disagree.
When you disagree, write a clear and respectful explanation. State the reviewer comment, explain your reasoning, and describe why you believe the original text is correct. If you have evidence that supports your position, cite it.
The response letter is the place for this explanation. Do not make the change in the manuscript and then explain in the response letter that you do not agree with it. That creates a confusing situation where the manuscript contains a change you do not support.
The Marked Up File as a Record
The marked-up file is beyond a convenience for the reviewer. It is also a record of the revision process. If a question arises later about what was changed and why, the marked-up file and the response letter provide the answer.
The National Library of Medicine hosts research-method references that describe how research records should be maintained. The same principle applies to manuscript revisions. Keep the original manuscript, the marked-up manuscript, the clean manuscript, and the response letter together in a single folder. This folder is your revision record.
The revision record is especially important if you are submitting a revised manuscript to a journal that uses a submission system with a limited number of files. You may need to upload the clean manuscript as the main file and the marked-up manuscript as a supplementary file. The response letter is usually uploaded as a separate file.
Common Failure Patterns
The most common failure is submitting a file that still has visible track changes. This can happen when the author forgets to accept all changes, or when the author accepts changes in one section but not in another. The editor will see the revision markers and may return the manuscript for correction.
Another common failure is a mismatch between the clean manuscript and the marked-up manuscript. The author may revise the clean manuscript after creating the marked-up version, or the author may create the marked-up version from a different version of the manuscript. The editor will see differences between the two files and may not know which one is correct.
A third failure is a response letter that does not match the manuscript. The response letter says a change was made, but the change is not in the manuscript. Or the manuscript contains a change that is not described in the response letter. This can happen when the author makes changes after writing the response letter and does not update the letter.
A fourth failure is a response letter that is too vague. The author writes "We have revised the manuscript" without saying what was changed or where. The reviewer cannot verify the changes and may ask for more information.
Practical Steps for Preparing the Files
The following steps describe a reliable workflow for preparing the clean manuscript, the marked-up manuscript, and the response letter.
First, gather the original manuscript and the revised manuscript. The original manuscript is the version you submitted for the first round of review. The revised manuscript is the version with all your changes.
Second, create the marked-up manuscript. Use the comparison feature in your word processor to compare the original and revised versions. Save the comparison as a new file.
Third, create the clean manuscript. Open the revised manuscript and accept all tracked changes. Delete all comments. Save the file as the clean version.
Fourth, write the response letter. Organize it by reviewer comment. For each comment, state the comment, describe the change, and explain the reason.
Fifth, check the files. Open the clean manuscript and verify that no track changes or comments remain. Open the marked-up manuscript and verify that it shows all the changes. Compare the two files to make sure they match.
Sixth, upload the files to the journal submission system. Upload the clean manuscript as the main file. Upload the marked-up manuscript as a supplementary file. Upload the response letter as a separate file.
Records and Measurements
Keep a revision log that records the date of each revision, the file name of each version, and the changes that were made. This log is useful if you need to reconstruct the revision history later.
The log should include the following information for each revision round:
| Item | What to Record | Why It Matters |
|---|---|---|
| Original manuscript | File name, date, version number | Provides the baseline for comparison |
| Reviewer comments | The full text of each comment | Needed for the response letter |
| Response letter | The full text of each response | Shows what you changed and why |
| Marked-up manuscript | File name, date, version number | Shows the changes in context |
| Clean manuscript | File name, date, version number | The final document for submission |
Professional Escalation Criteria
If you are unsure about how to prepare the files, ask the journal office for guidance. The journal office can tell you whether the journal prefers a marked-up manuscript, a response letter, or both.
If you are working with a coauthor who is not responding to your requests for revisions, escalate the issue to the corresponding author. The corresponding author is responsible for coordinating the revision process.
If you believe a reviewer comment is based on a misunderstanding of your study, you can contact the editor. The editor can clarify the comment or provide additional context.
If you are concerned about the integrity of the revision process, for example if a coauthor has made changes without your knowledge, contact the journal office. The Committee on Publication Ethics provides guidance on how journals handle disputes about authorship and integrity.
Welfare and Safety Context
The revision process is not a welfare or safety issue in the animal farming sense, but it is a matter of research integrity. The Committee on Publication Ethics describes the responsibilities of authors, reviewers, and editors. These responsibilities include honesty, transparency, and accountability.
The National Institutes of Health requires that research it funds be conducted with integrity. The revision process is part of that integrity. A clean manuscript that does not match the marked-up manuscript can raise questions about the integrity of the research.
Limitations
The clean manuscript and marked-up manuscript approach works for most journals, but not all journals have the same requirements. Some journals do not want a marked-up manuscript. Some journals want the response letter to be uploaded as a separate file, while others want it in the cover letter.
The EQUATOR Network provides reporting guidelines for different study types. These guidelines are not journal requirements, but they are widely used. When you revise a manuscript, check whether the journal requires you to follow a specific reporting guideline.
The National Library of Medicine hosts research-method references that describe how research is conducted and reported. These references are not journal requirements, but they provide context for the revision process.
Building a Revision Decision Framework for Each Reviewer Comment
A response letter that lists changes is not enough when a manuscript has dozens of comments across multiple reviewers. You need a decision framework that forces you to classify each comment before you touch the manuscript. This framework prevents the common failure where an author makes a change, skips a comment, or writes a vague response because they did not think through what the comment actually required.
Classify Each Comment Into One of Four Action Types
Before revising, read every reviewer comment and assign it to one of four action types. Write the classification directly in your revision log next to the comment text. This classification drives everything that follows, including what you write in the response letter and how you mark the change in the marked-up file.
The four action types are:
- Direct revision. The comment asks for a specific change that you agree improves the manuscript. You make the change exactly as requested or with minor wording adjustments. This is the most common type.
- Clarification addition. The comment reveals that a section is unclear or missing context. You add a sentence, a phrase, a citation, or a short paragraph to address the confusion. The change may not be a direct request, but it resolves the reviewer concern.
- Disagreement with rationale. The comment suggests a change you believe is incorrect, unnecessary, or based on a misunderstanding. You do not change the manuscript. You write a respectful explanation in the response letter and cite evidence for your position.
- Editorial or formatting request. The comment asks for a change to structure, labeling, table formatting, or reporting-guideline compliance. You make the change in the clean manuscript and note it in the marked-up file, but the change does not alter the scientific content.
The Committee on Publication Ethics core practices describe peer review as a dialogue where authors must respond to every point. Assigning an action type to every comment guarantees you have a response for each one. If a comment does not fit any of the four types, you have likely misunderstood the comment and should reread it.
Apply the Framework Before Making Any Edits
Work through the comments in order. For each comment, write the action type in your revision log. Then make the corresponding decision about the manuscript.
For a direct revision, locate the exact passage the reviewer referenced. Make the change in your working manuscript with track changes on. In the marked-up file, the change will appear automatically. In the response letter, write one sentence that states the change and one sentence that states why you agree with the reviewer.
For a clarification addition, identify the gap the reviewer noticed. Write the new text and insert it at the relevant location. In the response letter, explain that you added context to address the reviewer concern. Do not claim the reviewer asked for the exact wording you wrote. State that you added material to resolve the identified ambiguity.
For a disagreement with rationale, do not edit the manuscript. Write your explanation in the response letter. The National Library of Medicine hosts research-method references that describe how authors justify methodological choices. Use that same standard of evidence in your response. If you have data, a citation, or a logical argument that supports your original text, present it clearly.
For an editorial or formatting request, make the change in the clean manuscript. In the marked-up file, the change will show as a formatting adjustment. In the response letter, state that you adjusted the formatting or structure as requested.
Use the Framework to Build the Response Letter Structure
The action type determines how much space you give each comment in the response letter. Direct revisions and clarification additions get one to three sentences each. Disagreements get a short paragraph. Editorial requests get one sentence.
This structure keeps the response letter proportional to the actual work. A response letter that gives every comment the same length of text becomes bloated and hard to follow. A response letter that skips the reasoning behind a disagreement fails the transparency standard described in the Committee on Publication Ethics core practices.
Organize the response letter by reviewer, then by comment number. For each comment, write the action type in parentheses at the start of your response. For example, write "R1.2 (Direct revision)" followed by your description of the change. This labeling lets the editor scan the letter quickly and see which comments required substantive work and which were disagreements.
Cross Reference the Framework With the Marked-Up File
The action type also tells you how to mark the change in the marked-up file. Direct revisions and clarification additions appear as tracked insertions or deletions. Editorial requests appear as formatting changes. Disagreements produce no change in the manuscript, so you do not add any marker.
If you use margin comments in the marked-up file to label changes with comment numbers, only add labels for changes that exist. A disagreement has no corresponding location in the manuscript. Adding a label for a disagreement would create a marker that points to nothing, which confuses the reviewer.
The EQUATOR Network provides reporting guidelines that often require specific sections or tables. When a reviewer asks you to follow a reporting guideline, classify that as an editorial or formatting request. Make the structural change in the clean manuscript and describe it in the response letter. The marked-up file will show the addition of the new section or table.
Record the Framework Outcome in Your Revision Log
Your revision log should include a column for the action type. When you finish the revision round, review the log to confirm that every comment has an action type and a corresponding response. This review catches comments you missed or misclassified.
The log also serves as a permanent record. If a question arises later about why you did or did not make a change, the log shows your classification and your reasoning. The National Institutes of Health expects grant-funded research to maintain transparent records, and the same expectation applies to manuscript revisions.
Troubleshoot Framework Failures
The framework fails when you misclassify a comment. The most common misclassification is treating a clarification addition as a direct revision. A reviewer writes "This section is unclear" and you rewrite the entire section as if the reviewer requested specific wording. The reviewer only asked for clarity. Your rewrite may introduce new problems.
Another failure is treating a disagreement as a direct revision because you want to avoid conflict. You make a change you do not support, then write a response letter that says you made the change. This creates the confusing situation where the manuscript contains text you believe is wrong. The Committee on Publication Ethics expects authors to stand behind their work and explain disagreements respectfully.
A third failure is skipping the classification step entirely. You read the comments and start editing immediately. You respond to the comments you remember and miss the ones you skimmed. The framework forces you to process every comment before you edit, which prevents this failure.
When to Escalate a Comment That Does Not Fit the Framework
If a comment does not fit any of the four action types, reread it carefully. A comment that asks you to add a coauthor, remove a coauthor, or change the data analysis is not a standard revision comment. These comments touch on authorship and research integrity.
The Committee on Publication Ethics core practices describe how journals handle authorship disputes and integrity concerns. If a reviewer comment raises an authorship or integrity issue, do not classify it into the framework. Contact the journal editor directly and ask for guidance before you make any changes. The editor will tell you how to proceed.
The ORCID for Researchers page describes how researcher identity and contribution records are maintained. If a reviewer questions authorship, the editor may need to verify contributor roles. Your revision log and response letter become part of that verification process.
Apply the Framework to Data Management and Sharing Comments
Reviewers increasingly ask about data availability and sharing. The National Institutes of Health data management and sharing policy describes expectations for NIH-funded research. If a reviewer asks about data sharing, classify the comment as a clarification addition or an editorial request.
If your study already has a data availability statement, you may need to add a sentence that points to the statement. If your study does not have one, you need to write one and add it to the manuscript. The response letter should state where the statement appears and what it covers.
The framework handles this comment like any other. You classify it, make the change, and describe it in the response letter. The marked-up file shows the addition of the data availability statement.
Frequently Asked Questions
What is the difference between a clean manuscript and a marked-up manuscript?
A clean manuscript has no visible track changes, comments, or revision markers. It is the final document that the journal will publish. A marked-up manuscript shows every change that was made in response to the reviewers. It is a supplementary file that helps the editor and reviewers verify the revisions.
Do I need to submit both the clean manuscript and the marked-up manuscript?
Most journals require a clean manuscript and a response letter. Some journals also require a marked-up manuscript. Check the journal instructions for authors. If the instructions do not specify, submit the clean manuscript as the main file and the marked-up manuscript as a supplementary file.
How do I create a marked-up manuscript?
Use the comparison feature in your word processor. This feature compares the original manuscript with the revised manuscript and creates a new file that shows the differences. If you do not have the original manuscript, you can turn on track changes and manually reverse your edits.
How do I write a response letter?
Organize the response letter by reviewer comment. For each comment, restate the comment, describe the change you made, and explain why you made it. If you did not make a change, explain why. Reference the clean manuscript by line number and paragraph.
What if I disagree with a reviewer comment?
You can disagree with a reviewer comment. Explain your reasoning in the response letter. If you have evidence that supports your position, cite it. The editor will decide whether your response is acceptable.
What if I accidentally submit a manuscript with track changes?
If you submit a manuscript with track changes, the journal office may return it to you for correction. You can also contact the journal office and ask to replace the file. The journal office will tell you how to proceed.
How long should the response letter be?
The response letter should be as long as it needs to be to address every reviewer comment. A short response letter that does not address all comments is not acceptable. A long response letter that repeats the same information is also not acceptable. Be concise and specific.
What if the journal does not want a marked-up manuscript?
If the journal does not want a marked-up manuscript, submit the clean manuscript and the response letter. The response letter should be detailed enough that the editor and reviewers can verify the changes without the marked-up file.
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- Survey Design for Qualitative Research: Best Practices
References and Further Reading
- Research Methods Resources. National Library of Medicine.
- EQUATOR Network. EQUATOR Network.
- Core Practices. Committee on Publication Ethics.
- NIH Grants and Funding. National Institutes of Health.
- ORCID for Researchers. ORCID.
- Data Management and Sharing Policy. National Institutes of Health.
- NCBI Literature Resources. National Center for Biotechnology Information.
- PubMed. National Library of Medicine.
This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.