The trick is to make a few changes in the appearance.2da file. First of all you need to give the NPC an underwear model (modela) and a clothing model (modelb). It can be anything really but that should solve your problem.
Note that some npcs can't change their appearance without some modeling. Make sure that they have a custom head under the (head or heads) column in the 2da file. If they do, then they should be able to change their appearance with clothing and stuff.
Yell at me if you have any problems chief.
If its a Twi'lek, of either gender, it can wear any armor, clothing or robes in the game. And its likely that he might want the character to wear more than just normal clothing or underwear, so its best just to fill out the rows regarding what the NPC can wear.
Checking the tutorial here will definitely help:
http://lucasforums.com/showthread.php?t=148638)
And these too(to set up the head):
http://lucasforums.com/showthread.php?t=196778)
http://lucasforums.com/showthread.php?t=149992)