Do you make a bolt-hole specific sheet underneath, cut the bolt holes, bolt the parts down, and then cut the parts out?
Without knowing what the parts look like or what tolerances you're trying to hold, that sounds about like what I'd try. Particularly if it's going to be a repeat job.
Make a base plate with two or three tapped holes from each bolt circle that will be in your nested plate. If you had twelve parts, you would have 24 or 36 holes in your base plate.
Drill all the holes in your nested plate, then bolt the nested plate to your base plate and machine the profiles.
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