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is there any scanning software that can recognize manually highlighted(with a highlighter pen) areas of text and give an option to omit them from a copy of the scanned document?

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If you're still adding those highlights: some markers don't show on photocopies, so I assume such markers would not show on scans either. –  Arjan Sep 21 '10 at 19:57

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Most highlighter markers won't show up in a grayscale or black and white scan if you adjust the thresholds. At work we have our scanners set up to filter out the highlighter markers this way. We are out of luck with regular ink pen and pencil underlining though.

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You might be able to do this with OmniPage.

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