GaAs is grown embedded in pre-etched wells in the Si substrate. HNO3:HF, KOH:H2O and a dry etch technique are used as alternatives to form the wells. Cross-sectional SEM views of AlGaAs/GaAs heterostructures reveal the growth front and facet formation for the different sidewall geometries. Transmission electron microscopy is used to study epilayer degradation in relation to the substrate damage and the presence of edge induced defects in the GaAs. Cathodoluminescence reveals the uniformity of strain present in the GaAs layer embedded in the wet etched well. The impact of the different etching techniques on device integration is briefly discussed.