Simplest way I could figure was to screw a 3/4" piece of wood to a flat 8"x12" plank. The piece of wood gave me perpendicular surface for the flat side of the neck to butt up against. I clamped the neck to the piece of wood so that it could not rock...
I made a similar jig a couple of years ago for thicknessing neck heels with my Safe-T-Planer.
I also use it for drilling mounting holes in the heel like you.

Sounds like the only difference on my jig is I have 2nd piece of timber mounted to the bottom board that pivots and "clamps" from both side of the fretboard.

I'll and post a pic later if I remember.