Do MN files work after removing them from app?

Hey guys,

I’ve been using MarginNote for a little while now, but I’m confused about what do when I’m done annotating a file and want to archive it.

Here’s my process:

  1. I annotate PDFs in Study mode (I don’t understand the purpose of Document mode),

  2. When finished, I export my annotations as an OmniOutliner,

  3. I want to also archive my original PDF source files — that is, get them off of the MarginNote app and store them in DEVONthink, because

  • (a) it frees up space and file clutter in MarginNote (which doesn’t have a good file management structure) and,

  • (b) DEVONthink has better search capabilities which is useful for archived files,

As far as I can, there are two BIG problems with #3:

  • Exporting MarginNote-annotated PDF files are huge. They take up a ridiculous amount of space, so archiving them eats into my storage space when it involves hundreds of files (or more).

  • As far as I can tell — and I might be wrong about this — it seems to me that the MarginNote-created URL links don’t work when one removes PDF files from the MarginNote app. Is that right?

I’m hoping that it’s NOT true, and that there’s some way to solve this so that I don’t have to have all of my MarginNote-annotated PDF files constantly loaded on the app just so the MarginNote-created URL links will work!

Please let me know if there’s some way to export and archive MarginNote-annotated PDF files — that is, removing them from MarginNote after I’ve finished annotating them — while ensuring that MarginNote-created URL links still work. Thank you.

Like I said, it’s a big problem to archive MarginNote-annotated PDFs because of their large file size. However, I might not be able to use MarginNote if the MarginNote-created URL links don’t work after I export and remove files from the app.

Any solutions or suggestions? Thanks, everyone…


Can someone from @Support-Team , @Sushi_Support-Team , @Lanco_Support-Team , @Edward_Support-Team answer these questions??

This is what many @marginnote3 / @marginnote users have been struggling with for years, and are likewise seeking answers.

Many of us keep using the app because of it’s great features, but have been requesting solving problems with archiving files in exactly the way that @TinderTest has described here.

Some of us have also asked @marginnote3 / @marginnote related problems with archiving PDF files – and have seeking solutions for quite sometime.

We could really use your help solving these problems!



Thanks, @jprint

I just though of another question I meant to ask. I’m working on a collaborative project with colleagues. So, I’m wonder how I can archive some of MarginNote-annotated files on a shared folder (like a DropBox folder) so that my colleagues can click on the MarginNote-create URLs when they want to navigate to the sections of the text that I’ve annotated.

Is this possible? If so, what do I need to do to ensure this works?


I’ve tried to do this, but it’s always been with some difficulty.

As far as I know, all parties have to have MarginNote to have this work. But I’m not totally sure.


I concur with @jprint – this has been a long-standing problem for me, too, and I’ve been raising the very same questions that @TinderTest has raised here.

I’d likewise appreciate answers from the MarginNote support staff.

Thank you.



We’re going to need some guidance from the MarginNote team on this, but perhaps I can contribute a small point.

In general, there are a number of ways to link to PDF content via a URL. Some details (an old post, but still germane):

Note that you need a PDF reader that can parse the URI/URL and jump to the content. Depending upon how you want to specify the destination (i.e., do you want to have a URL to a specific highlighted passage of the PDF), it might be necessary for MarginNote to save the PDF with a named destination. This is a feature of PDF that is used to identify specific objects on a specific page, and is not the same as a PDF bookmark or page label.

At present, MarginNote generates an internal unique ID for each note. You can get this via the Edit > Copy note URL command. However, activating this URL opens MarginNote and expects the document to be present in your MarginNote database. Although I haven’t tested this personally (need clarification from the MarginNote team here), I believe you can only share it with others who (1) have MarginNote installed and (2) have the same PDF loaded, i.e., in the cloud.

To make the URL more “portable”, it would need to refer to the PDF file rather than be a MarginNote-specific URL, and, for example, include a named destination. Again, for this to work, a named destination needs to be added to the PDF. AFAICT, when MarginNote exports a PDF it does not currently add named destinations, or at least I’m not sure which export options need to be chosen to make this happen.

My sense is that the current PDF export mechanism for MarginNote needs improvement, such that there is an option to not flatten PDFs, and further, to add named destinations for each note. For simplicity, these could be the same as the internal UID for each note.

As a simpler alternative, and if you are willing to type out part of the URL yourself, you could just specify a destination page number (i.e., and share that.


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Thank you for your answer, @mobo.

I guess I should give a bit more background. I’m ultimately using my MarginNote-created notes in Tinderbox, which looks like some other users have been trying to do. So, I don’t want to in any way parse MarginNote-created URLs. I just want to use them, as they were created in MarginNote. Using MarginNote-created URLs represents one of the app’s most important features.

But I also don’t want to have to continuously keep my MarginNote-created documents on MarginNote – and on the cloud – just to use the MarginNote-created URLs.

It sounds like you’re saying in to do that we have to rely on MarginNote coming out with a better, more “portable” (or accessible) PDF export. Have I got that right?

By the way, does @marginnote3 @Support-Team ever respond to these queries? I put up this post last week, and no one there has even bothered to contribute. Seems really odd.

Thank you again for all of your input, @mobo

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Getting a response from @marginnote3 or @Support-Team has been an ongoing problem. Their support is somehow dysfunctional. Many of us are frankly pretty frustrated.

I can share what I know, but I’m just another user here. A real response should come from MN support.

To try to answer your question, yes, I believe the best solution, given your requirements, would be to export PDFs and share them via the cloud. However, this runs up against a known limitation in MarginNote.

To try to clarify the issue, let’s look at a typical MarginNote URL:


There are two parts: (1) the ‘protocol’ (up to the colon character), which indicates the MarginNote app, and (2) the path. The path has two elements: ‘note’ and a note ID. When this URL is resolved in Tinderbox or some other app, macOS is summoned to invoke the MarginNote app, and sends it the URL path. When MarginNote opens, it looks at the URL path, decides that a note is being requested, uses the note ID to resolve a specific note, and opens that.

In this fashion, you arrive at the precise note and highlighted passage of your document. Pretty neat.

However, if you try to open a URL for a note that doesn’t exist, nothing happens. MarginNote doesn’t report any error that the note failed to resolve. (You can test this by pasting a MarginNote URL into a web browser and changing the note ID.)

If you remove a document from your library via delete, the note URL will no longer work. As far as MarginNote is concerned, the note ID is now meaningless. Tbh, I’m not sure what happens when you select “Save in Historical Archives”, as there’s no documentation for this.

This is why I suggested the possibility of using URLs to a PDF, which could be resolved by many other PDF reader apps, and wouldn’t require MarginNote. You could export a PDF, delete it from MarginNote, but continue to share the annotated PDFs and links to specific parts of them. Henceforth the URLs would point to PDFs wherever you decide to share them, not to your copy of MarginNote. In this way, MarginNote would not be required by your colleagues. Again, though, there is a known limitation with the way MarginNote exports PDFs.

The MarginNote team is aware that PDF export is an issue for many of us. They haven’t yet given a clear answer about when or how it will be fixed (i.e., would the fixed PDF export assign named destinations to each annotation, or…?).



I am very sorry for the bad experience, and thank you very much for your contribution to the community, here I may need to clarify a few questions to you:

1. At present, MarginNote3 will not change any content of the original PDF. That is to say, the notes you make in MarginNote3 are stored separately in the database. When you choose to export the PDF, you can choose whether to export the notes you made. , But it does not generate a link to the note.

2. The link of your notes extracted in MarginNote3 can only be used between MarginNote3 and the software that supports URLs.

Finally, thank you very much for your suggestions, we will consider your needs

Kind Regards,
Support Team