Revision of the article after it is returned from a journal
Almost all scientific papers will be returned from a journal to the authors for revision before it can be finally accepted by the journal. That means, that you will get an email from the editor which will include some requirements from the editor himself or herself and also some comments from external peer review. It can be from one peer reviewer or from several.
It is a good idea to follow all these requirements and only if there are obvious misunderstandings from either the editor or the peer reviewer, then you may argue against the suggested changes.
You will then provide two new documents, a rebuttal letter to the editor and then the revised version of your manuscript.
In the rebuttal letter to the editor you explain in detail all the changes made to the manuscript, and you will give answers to all the critical elements given in a point by point list. The easiest way is to list the original text from the editor’s email and then under each topic exactly write what changes you have made to the manuscript.
In the revised version of the manuscript all changes should be clearly visible. You will typically use track changes in Word to illustrate what has been changed in the manuscript.
Remember to write (as always) in a positive tone in the rebuttal letter and avoid angry outbursts in capital letters or exclamation marks etc. Editors are nice people, and there is no reason whatsoever to get excited about professional criticism of your article. The end product will usually be better than before revision.