Originally Posted by It'sNotTheBike
Probably because the OP imagines the trained engineers who designed the air intake
botched the job, though those engineers had access to a dyno and more than likely spent
many hours making sure the airflow was optimized for the resonant cavity of the air box,
( think of Helmholtz and you will be on the right track).
How likely is it that the engineers did a bad job and someone who needs to ask how
best to cut holes in the air box will do a better job ? Sort of like leaving an orangutang
in front of a typewriter and waiting for the sonnets of Shakespeare to be produced
( don't hold your breath waiting for anything intelligible to come out of that typewriter ).
The goals of the engineers might differ from the goal of the OP. It is possible to tune the same engine differently to get different characteristics. I'm not saying going around drilling random holes in things is the way to go, but if you can manage to shove more air and fuel into an engine in the correct mixture, you will get a bigger boom and more power. Whether or not this produces undesired results by way of reduction of fuel economy, airbox noise, etc... is irrelevant; none of those things are (hopefully) the goal of the OP.
On the dyno comment, you do realize that the reason most people cut holes in their airbox is that they've purchased a jetting kit which requires larger airbox holes work properly? Most companies who make these kits such Dynojet or JD, also have access to dynos, and their results against the stock power curves can be seen.
Anyway, to answer the OP's original question, use a holesaw to cut out the corners then use a heated razor blade to cut nice straight lines between the holes. Optional is some sort of sanding wheel for cleanup after. You can see it illustrated here on a DRZ400S https://www.youtube.com/watch?v=VtKWbs0N5lo