3D printing on Atomic Level

[MartinPoets]

Precious metals cant be made (that would require transmutation)

If you could form take atoms and form molecules, wouldn't you be able to create metals, just like you could create anything else. Perhaps I'm just not familiar with what transmutation is.

[mechadense]

Transmutation means changing the atomic number of an element.
Some ways to do this are adding a neutron or an alpha-particle (= naked helium core) to the atomic core or smashing cores together.
Read up here to get more detailed informations.
http://en.wikipedia.org/wiki/Nuclear_transmutation

You absolutely can't use nanoscopic robot arms to transmute elements with alpha particles or other atomic cores for two reasons:
1) You can't hold a naked core it would instantly suck up electrons potentially destroying the structure of the robot arm tips
2) You can't overcome the enormous coulomb repulsion between the cores wich is orders of magnitude greater than the bonding forces between the atoms in the robot arm.

Neutrons cant be hold at all. At best they can be captured in cavities when they're ultra-cold.
You need a nuclear reactor for producing sufficient quantities of them.

Anyway,
With AP manufacturing systems there will be little need for precious metals.
With just carbon and a few other nonmetals (and appropriate nanoelectromechanical designs) many material properties will be emulatable.
You could call them advanced metamaterials.
The only thing you can't emulate with diamondoid nanomachines is digestability taste and odor.