This is a pretty obvious step but whatever. A more obvoius step would be to remove the side of your case before you begin cuting but again this it up to you. Unless your incredibly brave you might want to preclude this step with some thought and some measuring and marking and whatnot but after the step requring carefull thought you can go to the step requiring powertools . I used an adustible hole cuter set a little over 4 inches if you dont have one you could use a jigsaw or just a normal hole cutter fom your local home depot the adjustible one you can find at woodworkers warehouse. At any rate clamp the piece down very well, wear eye protection, be sure to lubricare with wd40, and most importantly take your time.
Step 2: Clean up metal/plastic filings
........ummmm i thinks this about covers it but just in case here is a picture
Step 3: Smooth the edges of the widow hole
Use a dremel and make things smooth this isnt exactly rocket science
Step 4: Cut the Plexiglass so that it fits in the hole
use the adjustible hole cuter without the center drill to make nice circular windows. make them a bit big and then sand them down to fit dont get over zelous like me or else they window won't fit perfectly. Be carefull because once you cut all the way through the windows has a way of flinging the like a frizby.
Step 5: Glue Plexiglass in and vola!!
Some people use silicon i used my trusty hot melt glue gun whatever works for you. Now you have port holes in your case tune in next week to sea how to add led case fans in the other side of the case. this is my first instructible so be kind .