Yesterday I asked this questions on physics part of stackexchange, but I was redirected to engineering side of the force ;-). We all know about the rapidly developing technology of 3D printing. However, this technology is still very very VERY SLOW. For printing objects larger than a matchbox you have to wait days. I wonder if technique and physics will ever allow us to create objects directly from the atoms, by manipulating the setting, structure and connectivity of atoms of a given element. If possible, how can we control the atoms so as to create a fast 3D printer?
A replicator is a very long way from 3D printing. Although 3D printing is often endowed in the media with quasi magical properties all it really is is multi axis CNC extrusion and not fundamentally different from any other CNC manufacturing process.
The key thing about the replicators in star Trek is that they can produce any material on demand from energy/elementary particles including very complex organic compounds (eg Capt Picard is often seen ordering 'Earl grey Tea : hot').
In this sort of context fabricating the shape of the object is fairly trivial compared to synthesizing the matter it is composed of.
There have been experiments in fabricating atomic scale objects using electron microscopes but this is still a long way away form making up complex molecules in bulk on demand.