When you create a new Drill operation, by the default height for Top and Bottom, are "From Hole Top" and "From Hole Bottom", respectively. With this default, the entire depth of the selected face(s) is machined - or if "Auto-merge hole segments" is enabled, it will machine the depth of the entire hole.
In some cases you may need to drill only a part of the depth of the hole, and (from HSMWorks 2011 R3) you can select e.g. "From Hole Top" for the Bottom height, in effect giving you the option to drill, say 1mm down from the top of every hole.
The following screen shot shows a few possible combinations of the drill height settings.
Bottom "From Hole Bottom".