How best to archive MarginNote-annotated files?

I work on very big, dense documents with lots of memory, so I like to import documents, annotate them, and then archive them.

While I greatly appreciate the robust annotation capacity that MarginNote provides, I still don’t understand how best to manage the flow of documents for these purposes.

In other words, because I annotate big, dense documents with lots of memory in MarginNote, I don’t want them to languish an clog up a lot of space in iCloud, especially considering that MarginNote’s folders and syncing remains glitchy.

I’m seeking advice on how best to do this – that is, archiving MarginNote-created files so that the URL links in such files (Word, DEVONthink, OmniOutliner, iThoughtsX) can still be used to refer back to the original text that link to the original text.

I expect other users which that there was a way that MarginNote-exported files were self contained so that a URL link could refer to a the text within a document, instead of having to rely on combination of MarginNote & iCloud to navigate back to the original text.

Anyway, I look forward to any ideas / suggestions for the best archival approach for MarginNote-exported annotation files, so that I can still use URL links that refer to a the text within a document (ideally, without having to rely on re-opening MarginNote & iCloud to navigate back to the original text) while also being able to unclog heavy files from MarginNote & iCloud after I’m done with annotating them.

Thank you for your assistance.


I’ve been plagued with the very same problems and questions, and am curious about insight from other users, as well as @Support-Team @marginnote @Lanco_Support-Team !

This seems to be a big workflow challenge / problem for many of us.

Thanks for raising this, @JournoProf !

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Thank you for your reply.

Yes, it has become a problem, and I’m desperately seeking a solution. So far, it remains a major bottleneck for my workflow. As I said, I’m grateful for MarninNote’s robust annotation features, but it does me (or other users) no good if I’m unable to archive those annotations with active URL links and have to rely on maintaining large documents in MarginNote folders and saved in iCloud.

Anyway, hopefully other users and MarginNote support staff can chime in with solutions.


Yes, this is one of the key reasons stopping me from adopting MarginNote as our main research note-taking tool (we analyse investments, so would typically read and annotate several >100-page annual reports, presentations and conference call transcripts per company). There should be a way to quickly organize and archive old notebooks and their associated files without clogging up space.


Thank you!

I’m very sad to say that I might be forced to abandon MarginNote because of this.

I had serious concerns about its inability to properly sync databases and documents between devices, but this is an even more fundamental problem.

Quite simply, if I’m unable to successfully export and archive MarginNote-created documents, it’s untenable for me to keep using the app.

I hope @Lanco_Support-Team and others will take note. In many ways MN is a wonderful app. But I suspect many more users will not use it if this problem isn’t corrected.

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@carlo Just out of curiosity, which annotation app do you use in place of MarginNote? Thank you!

I’d just use pdf text annotations that can be exported, saved on the cloud and searched. The MN workflow is much better, but some way to archive and retrieve old notebooks together with the associated books would be extremely helpful. My own app folder is already taking up >2G and I’ve only been playing with it…


Right. I hear you. So, are you just using the Preview app or something else that enables you to export your annotations? Thanks!

Like you, I prefer MarginNote’s workflow, but the inability to archive annotated documents, and use the MarginNote-created links once they’re offline, has become a serious problem. As I said before, it’s an untenable workflow approach for many users, especially for those of us who work on large files.

So far, it doesn’t appear that @Support-Team / @marginnote / @Lanco_Support-Team have responded to this issue, and so I fear they won’t address this problem – though I certainly hope they prove me wrong.

Baring that, I’m looking into other app solutions. Some of my students have suggested Highlights, which seems like it generally works, though I wish it would provide additional export formats (e.g., OmniOutliner). Do users have any other app suggestions?

Thank you for your assistance.


I believe I read some post in the forum saying full backup feature is going to be implemented soon. That may solve your problem.

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I actually don’t think that really relates to what we’re talking about here, but thank you.

@JournoProf There are many apps out there for PDF annotation. My personal favourites might be Skim and PDF Expert, but the workflow is totally different – outlining and summarizing has to be done separately and references annotated by hand (eg. “Investment properties – see AR2017 p. 78”).

I’m posting here because I’m hoping the programmers notice they have something that’s promising and useful to paying customers… if they just keep working on it and make a few improvements.

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Thank you @carlo! I’ve been looking at PDF Expert as well.

But, like you, I’m really hoping the MarginNote team will take note, and make changes accordingly. Many of us have been investing a lot of time in providing this kind of feedback so that they can become the kind of app that will ultimately serve their user, and get the attention and use that it deserves!

Ditto that!

Thanks, @JournoProf

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Quite welcome.

As you and @carlo said, I sincerely hope @Lanco_Support-Team and the MN development team heed the feedback we’ve provided, and come up with a solution. It would be a shame to abandon the app given what it offers and how much it has improved.

As you pointed out, by solving this problem (and fixing file syncing between MN platforms) will ensure that MarginNote "becomes the kind of app that will ultimately serve their user, and get the attention and use that it deserves! "

Here, here.

Thank you once again.

Sorry, these days are Chinese traditional festival Mid-Autumn (Moon)Festival. So I returned to my native town and sorry for delay the official reply on this thread.

I do attach great importance to you guys’ request @JournoProf @jprint .And we have a a special conference about your proposal. Currently, I’m going to write a technique technical realization report. Once I have details questions will notify this thread these two days.

We do appreciate your trust to marginnote. And strain every nerve to perfect Marginnote satisfying what’s our core users’ need. Since we have absolutely same vision of this software. Marginnote begin from developer’s personal studying demands and will never stop to aspire after visual learners important demands.Thank you!

Best regards,
Support Team


I’m very pleased to hear this news. Can you provided us a clearer sense of how things are developing on this front?

Thank you.

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Same question to @Lanco_Support-Team

I’m new to MN so only starting to experiment with it’s powerful features. However, I’m not new to managing a lot of information, including pdf, and the issue of archiving annotated pdf is central to my workflow. So far I have relied on GoodReader to annotate and export the annotations (mainly the highlighted text). Then I archive the annotated pdf in a database (TheBrain) where it will be inserted within its context.
So far I do not have too complicated needs in terms of archiving. I just need to be able to export the pdf with the highlights and other annotations, and be able to see those annotations in another pdf reader. Maybe my needs will evolve when I will know more about MN but I think the minimum would be to use/share the annotated pdf in another app.
Thanks anyway for the impressive work of developing this app.


That’s what we’re all hoping MN will do for us…

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