Hybrid nanostructures are attractive for future use in a variety of electronic components. Self-assembled hybrid organic/nanocrystals can couple quantum properties to semiconductor working devices and modify their functionality. For example, light absorption in some core quantum dot (QD)-based self-assembled detectors induces a large dipole. These dipole moments may change the current of a shallow field effect transistor on which the QDs' layer is assembled. In order to improve the absorption and quantum efficiency of such devices, multiple self-assembled layers are used. In such layers the charge transfer, excitonic energy transfer, surface trap passivation, and oxidation mechanisms are not fully understood. Therefore, establishing new tools for characterizing multilayer devices is essential. In the present work we have used confocal fluorescence microscopy to examine the photophysical properties of multilayered self-assembled organic molecules and QDs. We studied the interlayer coupling and surface-related mechanisms. By changing the coupling molecules and using photoinduced processes that gradually change the system, we were able to compare different binding groups and molecules under different conditions. Importantly, we found that in layered structures the binding group greatly contribute to the electronic coupling and luminescence, a contribution stronger than the linker's molecular length. Consequently, we propose that proper illumination of core QD-based detectors be used for activation and yield improvement. (Figure Presented).