If I have already finished drilling the hole, I either use a round file
or decide I really could use holes that are one size larger.
Sometimes I do both. Use a round file and then drill with the next
large size drill.

To avoid getting the holes in the wrong place: First center punch
where you want the hole. If you are a little off slant the center
punch and punch some more to move the depression to the right spot.

Next start to drill the hole with a small drill the thickness of the
web of the drill for the right size. If that is off, use the file and
drill with a somewhat bigger drill untill you get the hole centered.

If you are making the holes to mount something, try using a transfer
punch to get the locations right.

For thicker material there are a few more things you can do.

Dan