Book excerpt: The current state and perspectives in natural and life sciences are strongly linked to the development of novel complex organic-inorganic materials at various levels of organization, including semiconductor quantum dots (QDs) and QD-based nanostructures with unique optical and physico-chemical properties. This book provides a comprehensive description of the morphology and main physico-chemical properties of self-assembled inorganic-dye nanostructures as well as some applications in the field of nanotechnology. It crosses disciplines to examine essential nanoassembly principles of QD interaction with organic molecules, excited state dynamics in nanoobjects, theoretical models, and methodologies. Based on ensemble and single-nanoobject detection, the book quantitatively shows (for the first time on a series of nanoassemblies) that surface-mediated processes (formation of trap states) dictate the probability of several of the most interesting and potentially useful photophysical phenomena (FRET- or non-FRET-induced quenching of QD photoluminescence) observed for colloidal QDs and QD–dye nanoassemblies. Further, nanostructures can be generated by nanolithography and thereafter selectively decorated with dye molecules. A similar approach applies to natural nanosized surface heterogeneities.