We report a comparative study on selective epitaxy of nanostructures with different geometrical shapes. GaAs pyramids were grown by molecular beam epitaxy into circular holes, L-shaped holes, and cross-shaped holes, patterned using nanoimprint lithography. These GaAs nanostructures were used for guided-self assembly of InAs QDs. The results show that the initial shapes of the nanostructures have a strong effect on the nucleation of InAs QDs. Cross-shaped holes were found to be the most resilient against form changes when the height of the pyramid was increased. On the other hand the L-shaped islands became unusable for QD growths when more than twenty nanometers of GaAs was grown onto the patterns. Photoluminescence measurements on QDs embedded within the GaAs islands showed that the peak emission wavelength was similar for all types of pyramids. (C) 2011 Elsevier B.V. All rights reserved.