It is possible to create 2D machining operations directly from 2D drawings/sketches in Inventor HSM Pro. This can be useful if you have imported geometry from a DWG or similar, and do not wish to convert it to 3D to machine it.
For drilling, you can machine anything that is selectable as a point. You can select the points individually, by clicking on the model from within the Drill operations dialog.
Selecting individual points as drill geometry
Alternatively, you can add a number of Inventor Sketch Points to a new sketch to use as your geometry. Creating an Inventor sketch for groups of elements like points makes it easier to refer to these elements when used in multiple operations:
A sketch containing six Point entities
This sketch can then be selected directly as the geometry in the Drill operations dialog.
Selecting a sketch as drill geometry