If so, open the picture, select the magic wand tool (Tolerance = 32). Select one area of red, then go to Select -> Similar. It should select the rest of the red. Then just hit delete.
Facemaker was not designed to create faces with transparent backgrounds. If you want them transparent, you'll have to manually edit the background color out.
The other folders are for different layers of the same feature. Look at hat #10.. If you look in all 3 "hat" folders, you'll see 3 different parts (layers) of Hat #10.