I have the Testor's "Clear Parts Cement." I haven't used it much, but it dries clear if you get uniform coverage and just keep adding layers. I discovered this because I put a hole in a canopy. I wasn't trying to seriously fix it, it was past the point of no return. Anyway, I put some Scotch tape on the underside of the hole and just kept layering. It dimpled, because the tape is too flexible, but it is clear. I just took another look at it and it (AH-1W canopy hatch) fell off. (I didn't realize I was that ugly)
All jokes aside, test it first on a spare part. I think I understand what you're talking about, just follow the directions on the bottle and it should work fine. Then again, it depends what type of windows you want to make. We could probably offer better advice if you'd clarify a bit more. I think what Testor's is referring to are porthole type windows, etc. Remember- Test First! I hope this helps a bit. I have also heard of a way to make windows w/clear nail polish. Cheers, -Spencer