If you happen to have access to some Mould machines you could try: regular CNC - being the corners of the square not 90ยบ perfect angle, but with the radius of the last drill that you used. If it's a big hole, you can commit to have something like a 1mm round corners, Forget it if it's a very small hole!
Now the perfect tool for the job is: Spark erosion machine, you can Google it, basically they carve (with a CNC) whatever you want in graphite and that will be the template ( a bit like a stamper) then it's electricity, bla, bla, bla. So... for a square you'd only need a cubic stick of graphite and a Spark erosion machine (eheheh - easier said, than done! - My reahrsal room is in a mould factory and I allways think of making this to when I lokk to theese machines, but somehow never happened). Hope that all this talk helped somehow!
Cheers
PS - here's a pic of the Machined graphite: