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The short answer is no. You can't export the handwritting on the pdfs. When you view your annotations in the Sony reader desktop software, your just see a tiny little thumbnail of what the annotations look like, without the actual text behind it.
I've heard that the annotations are stored as simple SVGs, which can be extracted and viewed. But I don't know of anyone who has managed to re-align the annotations over the text.
One thing you can do is export the annotated text snippets (either highlighted regions or text regions touched by handwritting). This is pretty useful to build small summaries of pdfs. However, the device seems to have a hard time recognizing spaces in PDFs and the exported text is often missing spaces (all words concatenated together).
I have to say though, overall I do like the device for reading pdfs. It has a number of modes for reading single and double (and triple but I haven't tried that yet) column pdfs. You just have to make sure you have the device around if you want to view your annotations.
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