
This is just some aluminum angle stock that I've drilled 2 sets of holes. One for the single dots, and 2 for the 12th fret marker. I scribed a line so I can align the dot to the appropriate place on the fret board.

The fret board clamped to the jig

I just use a cordless drill with a bit of tape on the drill bit for a depth gauge while holding the jig like this.

Finished results.
I really like this over the other methods that I've tried, as getting the dot off even by a fraction of a millimeter looks totally crap. The whole process only took about 4 minutes including glueing in the dots. Much longer to write this tutorial.
Hope that it's useful to you.