Go to the Comment Menu and click the Comment and Delete. Obviously, you must know what to look for (rectangles can also be drawn by drawing single lines - a different command), commands like re can be surrounded by any number of spaces or line breaks. In this video, PDF Tutorial: How to delete any pdf document highlight by using adobe acrobat pro. In this example, removing lines 129 through 132 would remove 2 yellow rectangles. In order to remove such things you would have write a script that analyzes the contents source, locates those commands and removes them. The re commands in lines 129 & 131 draw rectangles, lines 130 & 132, fill them, line 128 defines color yellow, etc. You will then see this in object with xref = 5: What happens, can be seen when you decompress a page's /Contents object (either via PyMuPDF or via the MuPDF command line tool: mutool clean -d test.pdf test-expand.pdf). They indeed are no annotations, Whoever created the PDF, has decided to draw those rectangles permanently - very much as you would when using Page.drawRect in PyMuPDF.

How to remove highlight in pdf