You can make the handles transparent in the mc6 file as well just be setting the transparency for the handles to 1 and the transparency edge in the handles to 1, as well.  Those will be recorded in the .mc6 as long as you select the handles as part of the materials collection.

This is how you would accomplish this in the material room ...

Select the body handles material zone, change the trans and trans edge to 1.000, apply your material to the skirt zones but not the handles zone, save the material as a material collection and select all but the preview.  This will create an .mc6 file that will turn the handles invisible and apply the texture. 

Hugz from Phoenix, USA

Victoria

Remember, sometimes the dragon wins. Correction: MOST times.