Too many people are answering questions different than the one being asked. This isn't very productive. The question (re-phrased) might be:
Is there any digital fililing cabinet software similar to the NeatWorks software that is independent of a specific piece of hardware?
Guessing, specualting, talking about WIndows Drvers for scanenrs, etc., isn't helpful. Neither are answers from people who have no idea what Neat Hardware/Software does. If you don't have a reccomended candidate, or want to debate the question, you aren't being helpful.
Doing the same process by hand is missing the point. (The people who gave those answers are idiots.