You can open the auto circle dialog and then box select the group, but it might also grab the "bottoms" as well as the tops, doubling your return. You could try to skew the model before selecting them.
If all the holes are on the same face you can click on the face so it's highlighted and then shift click on one of the holes and it will create them all.
Copy past with pattern..... or...This is where you need some fancy level 3 programming with loops. Depending on your hole pattern ( or patterns ) you may only end with with a very small amount of actual " features "
you may use the quick feature option
follow these steps..
set default parameter of circle like depth, no of points etc
click on the surface o which holes are made
hold shift key and move the arrow on top corner of any one hole
you'll see a yellow colour circle on every hole on that surface. A left click and you are good to go
it will take you less time than reading this reply