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Atom-probe tomography of Ag-photodoped amorphous thin-film Ge40S60, the material of interest in nano-ionic memory and lateral geometry MEMS technologies, reveals regions with two distinct compositions on a nanometer length-scale. One type of region is Ag-rich and of a size typically extending beyond the measured sample volume of ~40 × 40 × 80 nm3. These type-I regions contain aligned nanocolumns, ~5 nm wide, that are the likely location for reversible diffusion of Ag+ ions and associated growth/dissolution of conducting filaments. The nanocolumns become relatively Ag-rich during the photodoping, and the pattern of Ag enrichment originates from the columnar-porous structure of the as-deposited film that is to some extent preserved in the electrolyte after photodoping. Type-II regions have lower Ag content, are typically 10–20 nm across, and appear to conform to the usual description of the photoreaction products of the optically-induced dissolution and diffusion of silver in a thin-film chalcogenide. The microstructure, with two types of region and aligned nanocolumns, is present in the electrolyte after photodoping without any applied bias, and is important for understanding switching mechanisms, and writing and erasing cycles, in programmable-metallization-cell memory.