I don't have a great answer offhand, but you may want to consider posting your question in the Custom Cover Art thread:
https://forum.blu-ray.com/showthread...0007&page=1341
While this tends to be more focused on people making and sharing custom covers rather than scanning existing ones, I'm sure some people there likely scan some elements at times and may know some tricks that could help you with the clean up process.
I do dabble in custom covers myself, but not nearly as much as some other people, and cleaning up scanned items is not one of my strong suits. But others they may be able to offer better advice in that regard than I could.