4D printing and some satanism
This is cheating a bit, but if you have antimatter available, you could rearrange it the same way as the matter in your base object is. Antimatter seems to follow all the same physics and chemistry as vanilla matter, it's just got opposite charges.
The requisite satanism is that you will need to employ the services of Laplace's demodemon. You need him in order to bypass Heisenberg's principle, so as to properly place every particle. Once you've made an antimatter copy of something, you can dispose of the original if you wish.
The whole process should work to convert antimatter into vanilla matter too.