I have a pair of 45mm 3/8" copper plates. I need to clamp a 41mm peltier module between them.

Any ideas how I could do it leaving each side flush? I thought of countersunk 1 or 2mm diameter 10mm long screws/bolts, but i can't find any. Pressing titanium u-channel over the sides might work if i could find some.

Know any place I can get custom cut plates?

if i am reading this right you will have to clamp both pieces of copper plate ,drill ,tap and use set screws. Most hardware stores will have all the things i mentioned.As for the copper plates i though you said you allready had those but if you want more try Rio Grande jewlery supply ( they are on the net ) most colleges that teach jewlery classes will have it in the book store or also try steel supply they might know or have it theimselves.
I ll be honest i am trying to picture what you are doing and the way this is posted it is confusing. Are you wanting the sides to be flush? you wanting the bolts to be flush ,you will not get anywhere trying to bend titanium that stuff doesnt bend and is wicked expensive. Draw a pic or something i might be able to help you out more seeing what you want to do.

I tried finding copper plate where you suggested, but stumbled on this awesome store. Can get everything from polycarbonate to titanium there.

Ordered a pair of 2" x 2.5" x 0.25" plates, $3.78 each.