Your terminoligy is getting you. First, example is if you want to put a hole through a part, you'll have a circle on a workplane and you will use the ""punch"" command and it will put the hole all the way through a part or list of selected parts (see below) Next, if you want to put a counter bore on an existing hole, you would have a circle on the workplane as shown below and then use the ""Mill"" command and give it a depth. Finally, if you want to do both at the same time, your workplane would need to be 90 degrees to the face that the hole and counterbore are in and then you'd create the outline (1/2 of the hole and the counterbore as shown), and the ""Bore"" it around the long axis. You can't really tell it, but that workplane and outline is in the middle of that part.