From Oak Ridge National Lab, we now have demonstrations of atom-by-atom, electron beam manipulation of silicon and graphene. These are early results and consequently rough, but do push the limits of nano-fabrication down into the single-atom regime.
References:
Dyck, et al., “E-beam manipulation of Si atoms on graphene edges with aberration-corrected STEM”, arXiv:1710.10338.
Jesse, et al., “Direct atomic fabrication and dopant positioning in Si using electron beams with active real time image-based feedback”, arXiv:1711.05810.