We combine focused ion beam patterning (FIB) and self-assembly of epitaxial quantum dots in order to produce regular quantum dot arrays. Island-shaped quantum dots are expected to nucleate at specifi c locations where the ion beam has formerly patterned the surface. Different ion beam patterning parameters are compared, including accelerating voltage, probe current, dwell time and pitch. Three different types of ion beam damage are explained. Secondary electron imaging (SEI) in a scanning electronic microscope (SEM) and atomic force microscopy (AFM) have been performed before and after overgrowth of the patterned areas. We investigate how the patterning parameters infl uence nucleation and overgrowth, including the diameter, height and distribution of three forms of structures formed, i.e. islands, rings and holes. Islands are preferably formed at arrays patterned at low acceleration voltage with low ion dose. Also, the relationship between patterning parameters and island sizes has been studied. Micro-photoluminescence was performed in and outside patterned regions, in order to compare their optoelectronic properties.