In this cross-sectional scanning tunneling microscopy study we investigated various techniques to control the shape of self-assembled quantum dots (QDs) and wetting layers (WLs). The result shows that application of an indium flush during the growth of strained InGaAs/GaAs QD layers results in flattened QDs and a reduced WL. The height of the QDs and WLs could be controlled by varying the thickness of the first capping layer. Concerning the technique of antimony capping we show that the surfactant properties of Sb result in the preservation of the shape of strained InAs/InP QDs during overgrowth. This could be achieved by both a growth interrupt under Sb flux and capping with a thin GaAsSb layer prior to overgrowth of the uncapped QDs. The technique of droplet epitaxy was investigated by a structural analysis of strain free GaAs/AlGaAs QDs. We show that the QDs have a Gaussian shape, that the WL is less than 1 bilayer thick, and that minor intermixing of Al with the QDs takes place.