Arrays of semiconductor quantum dots grown by selective area epitaxy, a process in which the size and position of the dots is determined by a lithographically patterned mask, can have a high degree of uniformity in both size and position. However, non-uniformity in the initial stages of growth causes broadening of the energy states of GaN/InGaN heterostructures grown using this technique, limiting their practical utility for device applications. A phase-field model was developed to simulate selective area epitaxy, accounting for a crystallographic-orientation-dependent deposition rate. Model parameters were varied to optimize the uniformity of the InGaN active layers. Conditions that led to the most uniform active layers included low total deposition rate, high surface diffusivity, low deposition of surface adatoms from the mask, and smaller contact angle at the mask-vapor-quantum dot interface. Other factors that improved uniformity were growth on (0001) substrates, which is the fastest growth direction, and more vertical orientation of the sidewalls of the mask holes. (C) 2012 Elsevier B.V. All rights reserved.