3D WindowManager using OpenGL

I’m working with a couple of guys to put together a three dimensional window manager for Linux using OpenGL. We have the window manger starting up the Xserver from the raw Linux terminal and booting up properly and have put together a little 3D environment you can move around in. The windows will be rectangular boxes.

Here’s the problem, is there any way to map a window created using XLib to a polygon? We’re trying to figure how to bind the two dimensional window to the front face of our 3D windows?