Here's a pic from my current build, the ancient, I mean classic, MPC TIE Interceptor. What I am doing is creating a template so that I can create new solar panels for the wings. The concept is the same for masking your canopy. First lay down the tape.
Now to create the template (mask in your case), I'm going to take a new #11 Xacto blade and cut along the inside of the framing (hold the knife gently, let the weight of the knife do the cutting). Once the excess is removed, this is what it will look like.
For you, your job is done. You've created a custom mask for your particular kit. From here, I would transfer the tape to a piece of sheet stock to create the needed solar panel and cut it out.
After I cut out the piece, I attached it to the model. Since I was using pre-scribed sheet stock, I left the tape on to prevent any chance of glue fingerprint making it's way on to the model.
After I was done gluing everything, I removed the tape and had a wing with new solar panels.
Were I planning on taking this kit to contest, I would have cut the panels slightly oversize and sanded them until I got a perfect fit.
Since I'm using this as a first attempt at scratch building a conversion, I'm happy with my work. I hope this answers your question (and gives you more ideas). If not, let me know and I'll break out my TIE Stryker canopy and do a better pictorial.
EDIT: Make sure you burnish everything back down before you paint. If you find that your mask didn't go all the way up to the framing, take a pointed toothpick or a piece of sprue and gently scrape away the paint. The wood or plastic shouldn't mar the clear.