Im not sure I understand. Are you going to put like a sunroof in it or something? Ive never actually taken the inner cover off to see what the structure looks like underneath. My guess is depending on how and where you cut you can keep its strength, but if you cut it the wrong way, you could end up with junk.
nm, you posted a responce already.
So you want to keep the front, middle and rear and basically remove the sides in two seperate peices? I suppose it could be done, but Im not sure how you are gonna deal with the window seals. If you leave the whole side as one piece and make your cut between the mount and the side seal, its might be possible. Some way to seal it all back up is gonna still have to be figured out. as well as a way to keep the 3 pieces together when its on the car.