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After scanning I need to manually check the text for scanning mistakes, remove folios and running heads and ensure that, apart from chapter headings and paragraphs the text runs on.
Assuming you have a rectangular text block and that folios, etc. are outside it, I would recommend you scan to PDF, batch crop the entire PDF (as with Acrobat Pro), and then do your OCR. That way you'll save yourself a lot.
Though it's been years since I've used ABBYY FineReader; maybe it already solves this problem for you?
Thanks John. I'll experiment.
Cropping the PDF, as John mentions, and reducing it with optimization will help get a cleaner scan. If you find it easier to edit/clean up the scanned text in Word, if you save the PDF into Word and clean up by making paragraph and character styles (and use them consistently) in Word, you can import into IDD and map your Word styles to IDD styles. Working in Word may make it easier to send to the client for review before layout in IDD, if that is part of your process.