It was already pointed out in 2018 that exported PDFs are too large and then in the same thread that the annotations they contain are not recognizable by other pdf readers.
Why has this not been addressed yet?
I feel cheated of my money and forcefully trapped with a product that doesn’t show any interest to integrate with the greater world of other applications and pdf readers. After spending hours on documents I cannot access the annotations anywhere except my iPad!
I agree. This is much needed and much overdue functionality. The annotations should be compatible with other PDF apps. Basic markdown encoding would be good, too.
Also agree. Plus the ability to export to markdown or formatted text - evernote is nowhere near as popular as it was and many people don’t use it. The Word export formatting is incredibly ugly. In order to get decent notes at the moment I have to export to a mind map app then export again as text.
Wow, I’m just learning about this issue. I’m glad I haven’t yet purchased MarginNote and haven’t made it into my workflow yet.
This is a deal breaker for me, actually 
I’ve been trying many apps for this purpose, including LiquidText and MarginNote, and I’m using the 14 days trial. I was really liking MarginNotes and I was considering going with it and buying it at the end of the 14 days, especially when I found out that if I imported an already annotated PDF it could recognize the annotations! I thought that meant that MN worked with standard PDF annotations.
But then I discovered that’s not the case and that every PDF I annotate with MN, when I export it, the annotations are flattened…
I registered on this forum just to express my support for this request. I’m a Windows and Android user, I only bought the iPad to be my digital notebook and to read and study work documents. If I can’t work with my files outside of my iPad and if my citation manager (Zotero) can’t read the annotations I make on my PDFs, this is a no go for me.
I ended up going with LT in the meantime and will probably only buy MN when this issue is solved…
I agree. I was about to plunk down money for MN after experimenting with it and LiquidText.
But there are a number of issues that has made me hesitate from purchasing and the issue with exporting of PDFs is one of them.
Since I would only be using LQ or MN for my own personal activities (i.e., non-professional) I am not in a hurry to buy either, so I am lucky that way. But, still, I would like to have a solid version of MN that I can purchase.
You’ve dodged a bullet! Liquid Text is a viable alternative, consider it’s annotations can be read by other apps and it even exists on windows now.
I sincerely doubt it will be solved, the developers apparently have a reputation of not listening to feedback based on other reviews. I never thought my experience with an app could spiral from 5 stars to 1.
Dear Developers,
@Support-Team @Sushi_Support-Team @Edward_Support-Team @Lanco_Support-Team @Relight_Support-Team
In case you check these forums, this request is still active! My annotations remain locked in those documents, your application was not exactly cheap either, kind employ better tactics to retain customers than to lock us in! You’ve made a great product but your ethics / business strategy is a stain on your reputation.
Hello
Sorry for the late reply. We are concerned about the data lockup you mentioned, and we currently have a full list for documenting and tracking all user requirements, of which the import and export modules are what we plan to focus on improving. However, in Marginnote3 phase, we may focus more on brain map and handwriting related optimization because of the limited resources of developers.
If you don't mind, would you like to talk to me about your workflow? For example, what do you need to do after you export a pdf of extracted data in general? Do you send the pdf to a Windows device? Currently Marginnote exports a flattened pdf copy, so for the time being you may need to export the excerpt information separately, e.g. export the excerpt to Word, where the hierarchical structure of your organization will be kept in Word in the form of an outline for your summary.
Kind Regards,
MarginNote-Edward
Support Team
That is a proper ‘non-answering’ answer.
For example, what do you need to do after you export a pdf of extracted data in general? Do you send the pdf to a Windows device? Currently Marginnote exports a flattened pdf copy, so for the time being you may need to export the excerpt information separately, e.g. export the excerpt to Word, where the hierarchical structure of your organization will be kept in Word in the form of an outline for your summary.
As we (myself, @xurc, @chai46, @JKF, @Spoon, @DrJJWMac, et al) have asked before, the workflow is that we want to save PDF files that are not flattened, i.e., we want PDFs with proper annotations that can be used with other PDF apps like Acrobat, PDF Expert, etc., etc.
Basically, we are just asking for standard support for PDF annotations, as described in § 8.4 “Annotations” of Adobe’s PDF Reference , v. 1.7.
To be honest, I’m not sure why we need to explain this in further detail. There are already quite a few posts on this forum about this issue.
Personally, I don’t use MS-Word and I don’t want MS-Word files. I only want proper PDF files or perhaps RTF files for interchange.
As it stands now, MarginNote does not really support this aspect of the PDF specification, and thus cannot inter-operate with other applications that handle PDF annotations. This lack of inter-operability with other apps has been a significant issue with MarginNote.
If the issue is how to encode MarginNote notes, which have a title and comments, you could use simple markup, i.e., # to represent note titles, etc. Add preferences to control the export formatting, if necessary.
My general request would be: please consider inter-operability a priority. I do not care at all about handwriting support, improved mind map, etc.
Thanks