First of all, don’t panic! We know you spent a long time putting your manuscript file together. Don’t worry, you won’t lose any of that time.
Next, check to make sure you’ve followed the Figure & Table Guidelines. In short, your figures should be in .TIF or .EPS format, and should be under 10MB each.
If your figures are in the correct format and are less than 10MB each in size, and the figures are visible, clear, and readable in your merged PDF, you can override the error message. For the editorial (pre-publication) process, the most important thing is that the Academic Editor and reviewers can see your figures. Once accepted, our Production team will be able to assist you with making any minor but changes to your figures.
However, please be advised that PLoS ONE does not have an author proofing step: you won’t be able to view the pre-publication formatted proof of the paper after it’s accepted but before it is published, so your paper should be as close to publishable as possible in every other respect.