Two methods come to mind:
1)Electrochemical machining (ECM) using a wire cathode and a 300 g/L NaCl electrolyte. see ASM Handbook, vol. 5, Surface Engineering or vol. 16 Machining.
2) Get some self-adhesive vinyl sheet (with peel-off protective backing). Punch the holes in the vinyl (maybe over some rigid cardboard), then attach to the steel and do some acid etching. It would speed things up if you can make your sheet the anode. HCl or warm sulfuric should work.
Hope this helps, & please give feedback.
Ken