Low temperature scanning tunneling microscopy was used to study the formation of single crystal nanostructures of Ag on Br-terminated Si(001)-(2×1) and their interactions with the surface at elevated temperature. Multilayer nanostructures were formed at 640K. They were facetted, and they exhibited highly-ordered surfaces that were imaged with atomic resolution to identify the 〈011〉 and 〈112〉 directions on Ag(111)-(1×1). Heating above 700K induced reactions involving Ag and Br and the desorption of AgBr. At these temperatures, contact between the Ag islands and Si(001) also led to Si dissolution in the islands, and three dimensional pits bounded by {113} facets were produced.