A surface layer of altered composition can play a key role in nanoscale pattern formation induced by ion bombardment

► Hexagonal arrays of nanodots can form when a binary compound is ion bombarded. ► We develop a theory that explains the genesis of these arrays. ► The species with the higher sputter yield is concentrated at the peaks of the nanodots. ► For a range of the parameters, the nanodot arrays coarsen as time passes.