I'm guessing this is something nanotechnology requires to make molecular devices. So, using the power of biological analogy I offer the following criteria for a functional assembler:
  • Sorting the right atoms and molecular fragments.
  • Holding onto these fragments for long enough.
  • Joining the parts together.
  • Releasing the assembled structure.
This cycle can then be catenated to further cycles until the device is complete. Some of the strange properties of the microworld that affect this construction are; heat, stickiness and charge. The sensible assembler works with these conditions, not against them. Indeed, the logic of tiny construction is very different from macro-scale devices - things can self assemble, make use of quantum mechanical effects and replicate themselves.

This has been an Infinite Monkeys contribution.