Will a nibbler work on Lexan windows without cracking it?
The hole saws are nice. Just watch it and play with speeds. It may melt and bind up on ya.
The cheap way is this: Use a compass to draw the hole you want to cut out. If you don't have a compass, then you may get by with placing the fan on there and poking a fine-tip sharpie through there and trace the inside diameter of the fan. You may not get the whole circle, but you can connect the dots and make the circle.
Then, rough out the hole. You can get a cheap sanding drum in there and sand the rest out. Even with a Dremel I do this. It melts, but as long as I keep the pressure on, it keeps going through like butter.
If it still needs some fine tuning, you can do so with normal sandpaper and your skilled hand. Just eyeball it out. Then you'll need to drill 4 holes for mounting the fan. That's pretty straight forward, but a pen won't fit down in the fan's holes. You can hold the fan down onto the window and lined up with the large hole you just made, then use the holes as a drill guide. Drill straight down as any side to side will either move the fan, or widen up the holes. Once you get one in there, it may be a good idea to go ahead and drop in the hardware for that first hole, then it won't move around and the other 3 will come out right.
You also don't need an big open hole. You could get creative here and just make some fat strips like a built-in grill. You could draw these out, drill holes at each end, then take a course file and connect the dots. I've used some drill bits that'll side cut lexan...and then some that won't.
Kinda like this:
But layed out a little better than that.