Engineering nanostructures with complete control over the shape, composition, organization of the surface structures, and function remains a major challenge. In my work, I have fabricated nanostructures using functional polymer motifs and nanoparticles (NPs) via supramolecular and non-supramolecular interactions. In one of the approaches to generate nanostructures, I have integrated top-down approaches such as nanoimprint lithography, electron-beam lithography, and photolithography with the self-assembly (bottom-up) of NPs to provide nanostructures with tailored shape and function. In this strategy, I have developed a geometrically assisted orthogonal assembly of nanoparticles onto polymer features at precisely defined locations. This versatile NP functionalization method can be used to fabricate protein resistant patterned surfaces to provide essentially complete control over cellular alignment, making them promising biofunctional structures for cell patterning. In another approach, I have utilized self-assembly of dendrimers and NPs without preformed templates to generate nanostructures that can be used as chemoselective membranes for the separation of small and biomacromolecules.