advice needed filling aircraft windows

My dad did it once by running a strip of masking tape behind the windows, and then filling them with putty.

I read about this method a while ago and liked it, though note the problems he ran into with losing some reference points.
http://www.airlinercafe.com/page.php?id=54

thanks for that, i was thinking about using some styrene and then filling the windows but your idea sounds better ta!

I occasionally seal off the windows in a fuselage by gluing the kit windows into place, then when dry, filing the window to contour (lets be honest most of them stick up just a little above the surface). Once that's done, I fill any cracks or depressions with body putty and sand that down when dry. If you do it right, you don't use as much putty and the area is actually stronger than the putty alone is.

Microscale makes a brush on product called "Microclear" which is perfect for your application. Apply it on the inside of the model. It looks like white glue before it cures to a flexible, clear film.