It can be done, with good tinsnips but you need wrists like a wrestler.
If you intend to do this, then strip everything out first. and that means motherboard PSU --the lot.
Even if you don't leave filings, there is no way you can cut the steel without using "lethal force".
A messy way but a compromise, might be to open the existing holes with successivly larger drills until the holes merge and you might be able to twist out some of the interstices.
A smarter job would be to use a powered nibbler, and you will need ear defenders if you do.
I'd leave it alone and just make sure the air can flow right through your box, with as little obstruction as you can.