Metrology for structural and electrical analyses at device level has been identified as one of the major challenges to be resolved for the sub-14 nm technology nodes. In these advanced nodes, new high mobility semiconductors, such as III-V compounds, are grown in narrow trenches on a Si substrate. Probing the nature of the defects, the defect density, and the role of processing steps on the surface of such structures are prime metrology requirements. In order to enable defect analysis on a (III-V) surface, a proper sample preparation for oxide removal is of primary importance. In this work, the effectiveness of different chemical cleanings and thermal annealing procedures is investigated on both blanket InP and oxide embedded InP trenches by means of scanning probe microscopy techniques. It is found that the most effective approach is a combination of an HCl-based chemical cleaning combined with a low-temperature thermal annealing leading to an oxide free surface with atomically flat areas. Scanning tunneling microscopy (STM) has been the preferred method for such investigations on blanket films due to its intrinsic sub-nm spatial resolution. However, its application on oxide embedded structures is non-trivial. To perform STM on the trenches of interest (generally © 2015 AIP Publishing LLC.