I've been trying different methods to colour the frames. I first tried exporting a quick time movie from Flash, then opening it with Premiere to export it as a filmstrip file to open in Photohop. The problem was that this way I ended up with the double amount of frames to colour in Photoshop, since Flash had exported them at a 12 fps rate.
So I've finally turned again to Flash to colour the frames there by importing this bitmap I'd previously created in Photohop and by applying it to each frame.
Then I've exported the file to a quick time movie with an alpha layer and I've worked on it with After Effects. I've add it some effects to make the texture look a bit more realistic and I've tried to create the transition from the rough wooden texture to the human skin, but I'm still not happy with it. I don't know why the video with the tree texture and the one with skin don't match when superimposing them in After Effects...
Anyway, you can see the result in the video above.