Bake Animation to Armature with geometry?

Hello,

I am hoping for a quick answer to this question if possible, ok here goes:

I am working with Motion Capture data (just like the c3d import script) to control the movement of my Armature. My armature has a character attached which has been carefully weight painted onto my armature. I need to bake the animation to the skeleton so I can make changes, but when I do this using the built in script, only the armature is duplicated.

How can I bake the animation onto my skeleton without losing the attached geometry? There must be a way otherwise the script would be pretty much useless!

Thanks for any help