You can use the visible property for bodyparts. If the entire part is hidden by clothing then just set visibility off in the  properties panel.

If part of thee bodypart is visible (like thigh in shorts) then use a transparency map. The pic shown is an example of turning jeans into shorts but you will get the idea.

 

The pic is three pictures , the render showing the jeans with transmap, the jeans texture map, and the transparency map ( white visible black transparent)