Well, on TNG they used B & W negatives with color gels sanwiched between plexi. The later seasons had theirs color printed on some kind of film or another (I think) and wither laminated them to the plastic then covered by smoked plexi, or something similar.
I have done some color printing on transparencies and used plexi and light difusion plastic to back light LCARS before. But I can only print 8.5" x 11", and I am shopping around for a place/material to do larger printings.