How to remove all highlights from pdf

Open the PDF in Preview. Press cmd+i to open the Inspector. On the Inspector's toolbar, click the right-most tool that looks like a pen drawing a line. That will show entries for all annotations. Using the cmd-key, click each entry that shows the partial Highlig… and when all are selected, just press delete (e.g. backspace) and then click on the PDF document itself.

All Highlights will be removed, providing there are no PDF restrictions in play.

There is no means in Apple's Preview to remove a Highlight annotation based on the number of its occurrences.

I also have an AppleScript that prompts you for the PDF and then removes all occurrences of Highlight annotations.

Apple's Preview and Adobe Acrobat Reader use different approaches to implementing PDF highlights. Currently, only PDFs that have been highlighted in Adobe Acrobat Reader grant access to that text string for comparison purposes and subsequent selective removal.

The text string, when a highlight is applied to a word in Apple's Preview is not returned for comparison and accordingly, one cannot selectively remove highlight annotations applied in Preview. The ability to remove all occurrences of highlights in an entire PDF document remains programmatically with Preview.