Take the clothing into the setup room and delete the bones from the clothing that you don't want.  I suggest that you leave one more body part/group past what the clothing itself has.  You might want to open the hierarchy editor as well when you are in the setup room, but before you delete any bones and disconnect the first one in a 'chain' that you don't want to use and move it to the body.  It will keep your JPs in order a little easier. 

Example:
an arm on a long sleeve shirt -- move the first finger joints from the hand to body.  Then delete the fingers.  Leave the hand. 

When done with the figure, leave the setup room...and save it back out the library. 
You will still need to rename the figure, check for any left over morphs/morph groups and extra materials. 

--Rebekah--