We are doing this why?
I wouldn't bother trying to cover up the holes, etc. I bet there are gaps where the 5.25" drive bays are. The question (if you even want to ask it) is do you want a case with positive or negative ventilation? If you have positive ventilation, you'll have more air coming in then out, negative is the opposite ofcourse. There are debates and theories about which is better, I'm not versed enough in either side to write about it.
Here is what I'd do. Remove any covering that you've put in place. Those holes are there for a reason, don't block them. (unless you ARE smarter then the Cooler Master engineers who built the case.) Just remove the stock fans and replace them with something faster/better. Remember that faster fans will output more noise, and those that move lots of CFM tend to output the most. Even if the fan itself is quiet, the moving air can/will be noisy. I'm not even sure if there are any 100+CFM fans, I tend to see 80 max. Even the almighty tornado maxed out at 89.something. Look for something in the 50-80CFM range, and try to keep the dba to around 30.