Are you thinking of just replacing the mesh with an acrylic panel, or cutting the panel into a different shape and making a large window? It's unfortunate that Raidmax used rivets to hold the mesh on. It kinda limits your choices of window shape and mounting. But, you can still mod the thing.
Drill the rivets out using an ⅛" bit. Remove the fan and the mesh. You can now layout your new window design by covering the entire panel with blue painters tape and then drawing your design on the tape. Use a jigsaw or rotary tool to cut the panel, finishing up the cuts with a file, sandpaper or one of the finishing wheels for your rotary tool.
If you opted not to cut the panel or have finished all of your cutting, it's time to cut and mount the glass. I've used both acrylic and real glass before. Acrylics are easier to work with and you can get them in a number of cool colors. I would suggest you look for cell cast acrylic though, because it's a much better quality and easier to cut without chipping or cracking.
Lay out the glass with the shape drawn on the paper covering. If you are going to use more rivets or trade up to screws or bolts, you will want to drill those holes first, before cutting the sheet to size. Drill the nearest edge first, so if you make a mistake, you can just move over an inch or two to try again without ruining a whole piece. Use a bit designed to cut through acrylic because some regular bits may damage it. Drill the holes slightly bigger than the fasteners so they won't bind and crack.
If you have a large hole to cut for a fan, you can tackle that in a couple of different ways. The best way, of course, is to use a holesaw bit in your drill. Be very careful and you will have a perfectly round hole for your fan. You can also cut a hole with a jigsaw, using a blade that is designed for use with plastics or a very fine bi-metal blade. Drill a starter hole near to the inside edge of the hole and hold the jigsaw firmly to prevent chattering and vibration. You can also use a rotary tool to cut the hole. File or sand the hole edge smooth for a finished look that will not need molding.
Now you're ready to cut the sheet of acrylic to size. Use a jigsaw or rotary tool for this too. If the window is square or has straight sides, use a metal or wooden straight edge clamped to the sheet to guide the jigsaw for perfectly straight cuts. Again, file or sand the edges smooth.
You can get screws, bolts or rivets for mounting the acrylic at any hardware or automotive store. For that extra bit of bling, you can get allen head machine bolts, nickel or brass plated -- you can even use copper rivets instead of the standard silver color. My preferred method of mounting, though, is gluing the window to the back side of the panel with silicone adhesive. It's clean and smooth and doesn't distract from the window or what's behind it.
A neatly done window can add style to an otherwise dull case. Whether you decide to design an all new window shape or use what Raidmax has given you, take your time and pay close attention to the details. You'll get plenty of comps and be proud of your accomplishment.
My Best R'gards, Grump
The Mad Modder