CdSe/ZnSe quantum dot formation is investigated by studying different steps of the growth. To precisely control the critical thickness of CdSe grown on a ZnSe buffer layer, the CdSe self-regulated growth rate in atomic layer epitaxy growth mode is determined by reflection high-energy electron diffraction (RHEED) measurements for a temperature range between 180 and 280 °C. Then, the two-dimensional-three-dimensional (2D-3D) transition of a strained CdSe layer on (001)-ZnSe induced by the use of amorphous selenium is studied. The formation of CdSe islands is found when 3 monolayers (ML) of CdSe are deposited. When only 2.5 ML of CdSe are deposited, another relaxation mechanism is observed, leading to the appearance of strong undulations on the surface. We also studied the evolution of the surface morphology when 2.7 ML are deposited, to study the boundary between those two phenomena. The influence of capping on quantum dot morphology is investigated. It is found that cadmium is redistributed within the layer during capping. Our results show that the cadmium distribution after capping depends on the capping temperature and on the strain of the CdSe layer. Cadmium incorporation after capping is also studied. It is found that the amount of incorporated cadmium depends on the strain of the CdSe layer before capping.