lostatsea - The Visioneer software (ie: PaperPort) is the scanning software. As I said before - I also have a Fujitsu scanner but I'm holding off using it because it is an upright scanner and I don't want the graphite to get into the track. So I'm using the Visioneer flatbed scanner. I can, in that way, clean the glass with a soft cloth and some lens cleaner.

J.Edward - that is an interesting way to do the yellowed paper look. I was thinking of taking a parchment background and making it semi-transparent. In this way I can apply another layer behind the parchment and whatever color I put back there modifies the parchment look to being that color. So a yellowed paper look would (as you probably know already) have yellow behind it.

I wonder if I increased the resolution from 300dpi to 600dpi if that would help out any. The scanner also has a "Remove Moire Patterns". That may be also causing problems since the trees are similar to Moire patterns. Maybe the software is getting confused and trying to remove the lines? That might be why some of the lines look white. Maybe it is trying to remove them?