Most often you replace head. Here you have tutorial how to do:
http://www.sharecg.com/v/33316/PDF-Tutorial/Franken-Anime-Tutorial.-(PDF-version

I used similar trick to make clothed figure combinig conforming clothes and clothed figure.
Such figure is RAM friendly, takes less space on HD then figure + clothes), moreover is easy to pose (easy pick up body part which is not hidden under clothes).
For example: load original figure, load conforming clothes and boots. Set org fig IK off. Zero figure with joint editor window. Conform clothes and boots to org fig. Export obj for new figure.
Usually I save obj with:
original figure: head, neck, chest, left and right forearm, hands, fingers, thumbs
conforming cloth: chest, collars, arms, forearms, abdonmen, hip, thighs, shins
conforming boots: shins, feet, toes

Import saved obj and go to the setup room. Load bones from original figures. If you used loose clothes it is possible that you need fix some joints.