We have investigated the effects of in situ and ex situ post-growth thermal annealing on the organization of InAs/GaAs quantum dot superlattices, which consist of regular arrays of InAs islands embedded in GaAs. Using large-scale and high resolution cross-sectional scanning tunneling microscopy, we have mapped out the spatial distributions of the island arrays and the positions of indium atoms located both vertically and laterally between the island arrays. Both in situ and ex situ annealing induce vertical and lateral dissolution of the islands, which in turn significantly affects the organization of the island arrays. Annealing-induced variations in the positions of the indium atoms between the island arrays have enabled us to directly measure indium–gallium interdiffusion and indium segregation lengths. We discuss the effects of residual strain on these processes, which are critical for the design of novel devices based upon semiconductor nanostructures.