Thin film functional hybrid materials composed of inorganic nanocrystals sequestered within a self-assembled template are important for a diverse range of applications, from sensors to device electronics. The properties of these materials can be “tailored” by control of composition over various length scales; the major processing challenges are associated with understanding and controlling external factors, such as confinement and interfacial interactions, that affect the self-organization process. Spin-cast polystyrene-b-poly(1,1‘,2,2‘-tetrahydroperflurooctyl methacrylate) (PS-b-PFOMA) diblock copolymer films can form a micellar structure, with a PFOMA core (PS corona), and are induced to undergo a transition by annealing in supercritical CO2; consequently, the PS segments form the core with a PFOMA corona. We show that functionalized Au nanocrystals, initially dispersed within the corona (the PS phase) of the micelles, follow the morphological inversion and become sequestered within the core, now composed of PS chains; the nanoparticles segregate primarily at the PS/PFOMA interface within the core. These inversion experiments were performed on nanocomposite films with thicknesses h ≤ 150 nm. Therefore, only one or two layers of micelles spanned the entire film. The nanoparticles were not distributed uniformly throughout the films but remained primarily near the substrate. Several competing factors determine the overall distribution of nanoparticles: the van der Waals interaction between nanoparticles and interfaces, favorable ligand−block enthalpic interactions, and the conformational entropy of the host chains.