Is this color you were spraying, or a clearcoat? If a color coat, you can try sanding with very fine sandpaper. When the paint is removed, you'll have some fog left on the surface, which has to be polished out with finer and finer sandpaper. However, the discovery of the effects of future means you do not have to polish it completely clear like we had to do in the old days. By the time you get to 1000 or 1200 grit, then applying future again clears up the fog.
If it was a clear coat that got on the transparency, and it is an older aircraft, you may not have to remove it. Older aircraft had canopies that fogged quickly if left outdoors and many old aircraft had pretty foggy canopies, depending on how frequently the ground crews could repolish them.