I just used OCR software to scan a document consisting of 20+ pages into Word 2007. The result is a bunch of pages with their own margins and indents. I appear to have been able to reset the margins, but things like indents appear to be relative to the margins. Therefore, reducing the margin size has caused some paragraphs to go off the left side of the page because the indent got set to a negative value. I'd like to clear all page-formatting and keep visual formatting like font face, font size, font color, bold, underline, italics, etc. This way, I can start from scratch and reformat the page layouts the way I want.
I'm not sure if that's option for you, but you could use other, plain-text-based format (like TeX or HTML) and try to filter out the information by a scripting language like Perl or Python, (or, provided that the output is "simple" enough, even using a smart text editor and regular expressions could do the job).
Note that while you can use Word to export to that format, but if you can use the format right away in the OCR software, I'd definitely try that one first. As a general rule for WYSIWYG editors, files exported in markup formats tend to be extremely complicated.