Hi,
Select the geometry,go and right-click "Feature-sets"(in Explorer at leftside of screen) and click "Make feature set" (I have a Finnish (partly) vers. of PM, so the commands might not be exactly how I have translated them ) Then right-click that feature set name,( It appears just like toolpaths etc.) and pick "settingts". That should open a form where you can choose whether you are making a boss or pocket etc. define Z-hights (top and bottom) of the feature. Click OK (might be accept or apply), and the feature is "extruded". Now yo can use 2D area clearance functions to make your toolpaths.
What version are you using?
Osmo P
PS. I have allways felt that Powwermill is a little bit glumsy with 2D
Caution for growing spindels