We present simulation for the morphological evolution of a Stranski–Krastanow system during the annealing process. By considering the strain energy, the surface-energy anisotropy, and the film–substrate interaction, the simulation demonstrates that the morphological evolution of the system can lead to an array of nearly uniform islands that is stable against coarsening. The stability results from the suppression of strain energy relaxation by strong surface-energy anisotropy and strong film–substrate interaction.

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Self-alignment of quantum dots separated by spacer layers is investigated by using a three-dimensional finite element method. We find that the morphology of the top islands is not just simply a reproduction of the buried islands. It is dependent on the arrangement of the buried islands, the interruption time, and the spacer layer thickness. If the buried islands are uniform and regular, with appropriate choice of their spacing and aspect ratio and with a thin spacer layer, there exists a regime in which the steady-state top islands are always uniform and regular, vertically aligned, and stable against small perturbations. For a thicker spacer layer, due to the change of the strain energy density distribution on top of the spacer layer, the top islands are misaligned with the buried islands. If the buried islands are not uniform and regular, our simulations demonstrate the top islands may self-assemble into more uniform and regular arrangements.