If the clear part is too large and needs to be trimmed or formed, I use 1000 grit sand paper to shape it. Then a final sand with 2000 grit finally painting with a drop of Future will make it clear again. If the entire lens needs to be colored, Tamiya makes clear red, blue, yellow, and green. Once formed and sanded, the Tamiya clear colors or future will bring back the clarity.
You can make your own clear parts by cutting, trimming and forming parts from excess clear sprues. Usung the method above also works very well.
I have also made them (on wings that do not have clear parts) with Liquidtex Acrylic gel. Typically I use the Tamiya clear paints for these.
Finally, For larger clear parts that have scuffs on clear canopies or if the canopy has a seam down the middle. (sanding the seam down with 2000 grit sandpaper) I have used the polish that is used to polish the headlight covers on cars. A small drop of the polish on a dremel tool buffing wheel and low RPM (between 500 and 1000), apply light pressure to polish the surface. If you use this to polish the canopy, you will need to wash it with mild dish soap to remove the polish residue so the frame can be painted.