We investigate the growth of InAs quantum dots on patterned GaAs substrates. The GaAs substrate has been structured using holographic lithography. Quantum dot formation along the patterns has been observed as well as an increase in homogeneity of the quantum dots. Furthermore, the use of ion beams focused to nanometer diameters for substrate patterning has been studied and showed promising results. For the investigation of vertically aligned InAs quantum dots, cross-sectional atomic force microscopy has been successfully employed.