Aside from adjusting your brightness and contrast, you could go in there manually with the eraser tool to clean it up a bit before putting a filter over top.

Also YAY SKWERLS <3

Thanks for the advice, hopfully ill have smexy scans in no time!

FEAR MY SQUIRRELLY WRAITH.

Also, when my mom was still around she used to be secretary and co-founder of the Blind Squirrels bowling league here in town. :3

awww these are so adorable x3

Oh and on the scanner issue...Hmm back then when I still had to scan my stuff I found it was useful to adjust the scanners brightness. When making it really bright the scanned paper appears as solid white and you should still be able to see the outlines - the lines might kinda break at some edges that way though. At least that state is nearly perfect for inking/coloring digitally then, because else you'd have problems with varying shades / colors of the paper itself which the scanner might have picked up.
well...Probably not that helpful of an advice but I tried ^^

photoshop > desaturate > auto levels > wand tool > eraser. adjust the wand tool's sensitivity to whatever works.

thats what i do. it works alot better on inked drawings though. oh, you could also go in to selective color and select the whites and make them whiter.

They're adorable. And they look delicious! *purr* :XP

hehe thank you. But don't eat them!