Is there a process faster than masking frame by frame for cutting an animated character from a background?
You can also checkout some of the various keying techniques. I've been able to color key things pretty well in After Effects or Nuke - for After Effects you can either use "Change to Color" to create a matte or "Linear Color Key". Either way you're going to need to split up the video into a bunch of layers - each one keying in (or out) a specific color. The end result you're going for is a black-and-white matte which you can use to cut out the footage. Often times it requires a combination of all kinds of techniques - keying some colors, luminance based keying (which can be done with "extract" in After Effects), luminance based keying on specific channels (also "extract") and a bit of hand-made roto.

If you need a more in depth explanation let me know.