Or if you don't want any holes in either side you could create a nest using dowel pins..
What shape is the outer profile of the work piece?
Ie, fix a slave plate to the table, if your work piece is square say 100mm x 100mm datum point middle middle, You know the edge is X50Y50X-50Y-50, using a 6mm spot drill, drill 6 locations at X53Y25, X53Y-25, X-53Y25, X-53Y-25, X0Y-53, X0Y53, place 6 dowel pins in these holes and then place your work piece in between them, and it will be square not matter which side you flip it and clamp accordingly. Also remove the pins if you plan to m/c the outer profile.
Obviously depending on what material you use for a slave board, will depend on your drilling process.
I use a type of model board called prolab or ureol, it's v robust stuff, you can easily drill a spot into it and the pin will be a nice tight fit, without having to drill n ream.
Also depending on the outer profile, that will dictate whether you need to programme it using cam or do it manually.