Using scanning tunneling microscopy and spectroscopy we have studied both the geometric distribution and the conduction properties of organic shell capped CdSe nanocrystals adsorbed on hydrogen-passivated Si(100). At submonolayer concentrations, the nanocrystal distribution on the surface was found to be highly nonhomogeneous, with an aggregation of most of the nanocrystals into islands of monolayer thickness. I-V spectra collected on nanocrystals adsorbed on n- and p-type substrates showed a strong difference in the conduction behavior, caused by the substrate: CdSe nanocrystals on n-Si:H caused a widening of the surface band gap by 1 eV with respect to the gap of the substrate, while a significant narrowing of the gap was observed for nanocrystals on p-Si:H. This experimental result could be explained by modeling the system as a metal-insulator-semiconductor (MIS) diode. Using this model we have found that the current through the MIS junction is limited by the nanocrystals only in one bias direction, while in the other bias direction the current is limited by the semiconducting substrate. This property may be of relevance for the construction of hybrid electronic devices combining semiconductor electrodes with nanoscale elements such as nanocrystals or organic molecules.