I use a drill press for most interior holes.  For those beyond the radius of the drill press I use a hand held small rotary tool.  The problem is to make it a true perpendicular cut without it going to a slight angle, thus sometimes making close cuts with the scroll saw having to be done very carefully, and sometimes the bottom stack of wood needing some cosmetic work.  What is a simple way of doing the interior holes that are beyond the radius of the drill press, that are perpendicular without having to eye it?

 

Mel