AbstractLarge-scale assembly of individual atoms over smooth surfaces is difficult to achieve. A configuration of an atom reservoir, in which individual atoms can be readily extracted, may successfully address this challenge. In this work, we demonstrate that a liquid gold–silicon alloy established in classical vapor–liquid–solid growth can deposit ordered and three-dimensional rings of isolated gold atoms over silicon nanowire sidewalls. We perform ab initio molecular dynamics simulation and unveil a surprising single atomic gold-catalyzed chemical etching of silicon. Experimental verification of this catalytic process in silicon nanowires yields dopant-dependent, massive and ordered 3D grooves with spacing down to ~5 nm. Finally, we use these grooves as self-labeled and ex situ markers to resolve several complex silicon growths, including the formation of nodes, kinks, scale-like interfaces, and curved backbones.