We analyze self-assembled nanocrystals of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) molecules on hydrogen passivated Ge(0 0 1) surfaces with use of scanning tunneling microscopy (STM) and spectroscopy(STS). At 0.7ML coverage, 2.1 nm high, elongated, hexagonal islands inclined at 37 degrees with respect to the substrate row are mostly observed. By measuring the differential tunneling conductance, we observe an effect of electronic decoupling of the nanocrystals due to the introduced passivating layer. Finally, we shortly discuss the stability of the islands and their interaction with the scanning probe in the ultra-high vacuum environment. (C) 2015 Elsevier B.V. All rights reserved.