Combining inorganic and organic components to create functional materials has been an active area of research in recent years. Inorganic components possess useful electric, photonic, or magnetic properties while organic components can self-assemble into a variety of morphologies on the nanoscale. We describe a novel approach for arraying nanoparticles using a modified diblock copolymer scaffold. Thin (30 nm) films of poly(styrene-block-methylmethacrylate) (PS-b-PMMA) copolymer were used as a substrate. Upon annealing, PS-b-PMMA forms lying-down cylinders of PMMA in a matrix of PS. These thin films were modified by exposure to ultraviolet light in vacuum which photochemically thinned the PMMA, creating a more highly corrugated surface. We find that colloidal superparamagnetic FePt nanodots and semiconducting CdSe nanodots deposited on this surface show a strong preference for the photochemically modified phase. This hierarchical self-assembly method may prove useful for many nanomaterials-based applications.