Not being that familiar with the Stuka I looked up a picture and found this:
http://www.rlm.at/galerie/17/Stuka-Winter-4.jpg
I assume you are talking about the round panel that the rear gun mounts through.
If the canopy has a rasied ridge where the circular part is, stick a piece of masking tape over the whole window (I recommend Tamiya tape because it is very thin and sticks very well), burnish the edges down toghtly against the ridge (use a finger nail, toothpick, or a burnishing tool). Use a sharp (read that as "New") #11 Xacto knife and slowly and carefully cut the mask out. Lean the knife so it pushes in toward the ridge and it will follow it pretty well.
Otherwise, you can get circle cutters, similar to a compass that holds an Xacto knife blade that would do the job. You could also find two objects (coins, perhaps) the proper size and cut around the edge of them with a sharp Xacto knife. Cut one piece solid for the inner mask and one that is a large hole for the outer mask.