Remove existing PDF highlights (not MN3 highlights)

I imported a PDF with highlights already in it. They appear as blue highlights that I can not seem to get rid of. How do you erase existing PDF highlights?


What app are you using to highlight the text in the pdf? Can you send a screenshot ?

Kind Regards,

Support Team

This should work:
Open the imported pdf in any pdf editor that can read and write regular pdf highlights, remove the highlights there and then reimport the pdf to MarginNote.

Thank you. I will try that.

I am a little unclear on how MN3 is working behind the scenes with documents and mindmaps. If I have a PDF with a 300 node related mindmap, remove the PDF and clear our the PDF-only highlights, and reimport it, how does MN3 reattch the 300 nodes to the correct part of the PDF? Would seem, from a CRC point of view, it’s a different file. Curious too if I just import a totally unrelated document like War and Peace – what does MN3 do with those 300 nodes? (Scared to try it as I am unclear exactly what is taking place / where things live.)


I’d encourage you to clone the map to have a backup and then experiment with different scenarios.

In general, there are two separate types of highlights when looking at documents in MarginNote: pdf annotations created with a traditional pdf editor and excerpts created with MarginNote.

Pdf annotations can actually be converted to excerpts via import → pdf annotations. Now the document contains both pdf annotations and excerpts.

Excerpts can be removed anytime within Margin Note, but pdf annotations can’t be edited or removed without a third-party pdf editor.

Excerpts can live only in the document or they can also be added to a notebook. In the second case, the document becomes bound to the notebook.

When a notebook (mind map) has excerpts from a document and that document is removed, then the relation still exists. It’s just that the document can no longer be found.

However, after removing the document from MarginNote and then adding it again, the link between notebook and document is automatically re-established if it is the same document.

In cases where this doesn’t work, there is a “rebind” function where the user helps MarginNote find the right document and re-establish the link.

Afterwards, selecting an excerpt once again opens the document from which that excerpt was created.

Hope this helps.

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That helps so much! Thank you greatly for taking them time to write that up. It really helps me.

I love MN3 / just making sure I am understanding where the data actually is, is backed up, etc. so as to not accidentally kill days of work / reading.

Sure wish the creators would write a definitive / exhaustive user guide.

You’re welcome :slight_smile: