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I always use the "remove headers and footers" option when saving to Word in FineReader 9. It often misses one or two headers or footers in a book, but that's better than removing them all manually. Never had any trouble with it removing anything it shouldn't.
That said, after scanning some 50 books I'm still learning. It is a heck of a lot of work, most of it occurring after the actual scanning.
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