Nanostructures are likely to become primary components of future electronic devices. Self-assembled hybrid organic nanocrystal devices are a route to achieve this goal. One central issue in using molecules in such devices deals with applying measurement methods which locally probe the molecular device. In this work we investigated hybrid molecular semiconductor quantum dot devices using cathodoluminescence measurements. A narrow cathodoluminescence peak was detected at proper conditions. This narrow resonant-like peak was found to be sensitive to the substrate material and its doping, to the nanoparticle sizes, and to the organic molecule linkers. The peak is assigned to resonant charge transfer from the charged nanocrystals to the deep surface states of the substrate. This suggests that cathodoluminescence measurement may probe the charge transfer in the hybrid device.