The Editors' response after your paper has been peer reviewed should be read carefully. While it may sound like a rejection, it may be an invitation to resubmit the paper with revisions, and sometimes after additional experiments have been done. Most referees will attempt to make useful criticisms intended to improve the quality of the paper, and their comments should therefore be seen as such, and not as personal criticism.

You should make the necessary changes as soon as possible (most journals will give you a deadline). Return 3 copies of the revised text (and new figures if any), with a covering letter that gives clear responses to all of the referees comments. Respond to each point made (numbering the points helps), and clearly state where the text was revised appropriately.

example:

Response to reviewer 1:

"Thank you for your valuable comments and suggestions. In response to the points that you raised, I would like to offer the following answers.1. We agree with point 1 that this sentence is unclear, and have revised the text on page 4, paragraph 2 accordingly".

You are obligated to make all of the changes recommended by the reviewers, but if you strongly disagree with a point you must give a clear argument for the editor as to why you disagree. Be diplomatic in all of your responses.