you'd do that with a dremel tool, and be very careful.
If you twist the knife around as you press into the plastic it should make an hour glass shape, but that's ok, just spin it around unitll the hole looks a litle rough. make sure to use a sharp blade for small holes... for something like a Master grade kit with 90mm cannon holes, use a dull blade, or one where the sharp tip is snapped off. I use this method from time to time, It looks good on wargaming miniatures, so I think it should be ok for everything else. just don't overdo it.