In my experience one revised manuscript should contain changes marked with color (Red, Blue, or green etc) and another copy of the manuscript has changes but changes are not marked with another color and should be black. The real meaning of that statement can be explained by that editor of the journal.

Hi Arif,

A clean version of the manuscript is one that reflects the final product with no additional marks/comments. If you're working with Microsoft Word, this requires you to "Accept" or "Reject" all tracked changes.

The two versions - tracked and clean - are useful to journal editors for different purposes:

The tracked version allows him/her to quickly identify which sections have been modified with grammatical changes, corrections, or new text since an earlier submission. This is commonly used to check if/how an author has incorporated feedback from reviewers. Some journals will also require a supplemental cover letter that provides a point-by-point response to the reviewer's feedback.

The clean version allows the journal editor to read the manuscript in its final form without distraction from revision history. If all the reviewers comments haven been satisfied, the managing editor will usually re-read the manuscript in its final form to confirm it is ready for publication.

Best wishes for success!

Hamed Bazaz

Founder, Managing Director | JournalEdit (journaledit.com)

Submission Instructions

If you are submitting a revised manuscript, upload your revised submission to the submission system and include the following items:

• Response to reviewers: Address the specific points made by each reviewer. Include your responses to all the reviewers’ and editors’ comments and list the changes you have made to the manuscript. Upload this as a “Response to reviewers” file.
• Revised manuscript (marked-up copy): Include a marked-up copy of your manuscript file showing the changes you have made since the original submission. The best way to show these changes is the “Track Changes” option in Microsoft Word. Upload this as a "Revised Article with Changes Highlighted” file.
• Revised manuscript (clean copy): Upload a clean copy of your revised manuscript that does not show your changes. Upload this as your “Manuscript” file.
• Reference: https://journals.plos.org/plosone/s/revising-your-manuscript