Optically active, highly uniform, cylindrical InGaAs quantum dot ͑QD͒ arrays have been fabricated using nanosphere lithography combined with Bromine ion-beam-assisted etching and molecular beam epitaxy ͑MBE͒-assisted GaAs mass transport. Previously fabricated QD nanopillar arrays showed significant degradation of optical properties due to the etch damage. Here, a novel mass transport process in a Riber 3200 was performed to encapsulate the lithographically defined InGaAs disk QDs in a GaAs matrix, resulting in the passivation of the etch-damaged QD sidewall layer. Photoluminescence emission intensity following the mass transport process increased by a magnitude of 4-10 as compared to that from unprocessed nanopillar sample. In addition, a PL peak energy redshift was observed after mass transport, presumably due to the decrease in the lateral barrier potential from vacuum to GaAs, as well as the elimination of the depletion layer. Furthermore, the mass transport process in the high vacuum MBE environment enables GaAs overgrowth with few defects and dislocations following mass transport for surface planarization. PL emission intensity increased by an additional factor of 4 following GaAs overgrowth, bringing the QD intensity to 1 2 of that of the original single quantum well. Thus, the potential of the MBE-assisted mass transport process has been demonstrated to fabricate high optical quality InGaAs quantum dots encapsulated in a GaAs matrix for device applications