In the previous post on this topic I overlooked excellent work from Vienna. The authors claim to demonstrate precise control over the motion of individual silicon atoms across a graphene substrate by STEM. Differing from the Oak Ridge effort, this work uses lower e-beam energy and single-site dwell of ~10s at each successive carbon atom target location. The speed is already competitive with STM methods, but does not require cryogenic temperature.
Reference: T Susi, M Tripathi, J C Meyer, J Kotakoski, “Electron-beam manipulation of Si dopants in graphene”, arXiv:1712.08755.