Printers are sold with an embedded chip that prevents the printing of currency. From what I understand, the chip is typically buried so deep into the printer that they simply can't operate if you could find it and remove it. We could attempt a similar requirement on a 3D printer.
The cat is out of the bag already. Several of the hobbyist 3d printers are self replicating. You're also selling a device to a market which is inherently prone to tinkering and modifying things. It wont last long.