I've set awkward shaped parts into glass bedding compound to be worked on, like drilling, tapping etc..
Bondo for holding parts for engraving works well but I like something tougher for machine work.
I use the glass bedding for holding parts for engraving too if I'm doing a number of the same parts.
Probably overkill on my part, but that's the way I've done it.
A piece of squared up hardwood for the backer.
I use release agent on the part. Otherwise it's a tough go of it to get things separated and cleaned up afterwards!
To make sure the part doesn't move from it's cavity while working on it, I use either a couple of small clamps that I move around as needed as I work,,or sometimes a simple bar strap clamp or two accross the piece where needed and screwed down with a drywall screw on either end secures it fine.
Make the wooden block large enough to accomodate the clamps, screws, etc and deep enough to allow a firm grip in the drill press/mill vise.
Drilling,reaming,tapping thru the metal, compound and into the wood doesn't damage any tool bits.
With any luck, you can make use of the mould again on an identicle part than needs fixing.