The controlled organization of nanoparticle (NP) constituents into superstructures of well-defined shape, composition, and connectivity represents a continuing challenge in the development of novel hybrid materials for many technological applications. We show that the phase separation of polymer tethered nanoparticles immersed in a matrix of a chemically different polymer provides an effective and scalable method for fabricating well-defined submicron-sized amorphous NP domains in melt polymer thin films. We investigate this phenomenon with a view toward a better understanding and control of the phase separation process in these novel "blends". In particular, we consider isothermally annealed thin films of polystyrene-grafted gold nanoparticles (AuPS) dispersed in a poly(methyl methacrylate) (PMMA) matrix. A morphology transition from discrete AuPS domains to bicontinuous to inverse domain structure is observed with increasing nanoparticle loading, consistent with composition dependence of classic binary polymer blends phase separation. However, the phase separation kinetics of the NP polymer blends exhibit unique features compared to the parent PS/PMMA homopolyiner blends. We further illustrate how to manipulate the AuPS nanoparticle domain shape, size, and location through the imposition of an external symmetry-breaking perturbation. Specifically, topographically patterned elastomer confinement is introduced to direct the nanoparticles into long-range ordered submicron-sized domains having a dense and well-dispersed distribution of noncrystallizing nanoparticles. The simplicity, versatility, and roll-to-roll adaptability of this novel method for controlled nanoparticle assembly should make it useful in creating desirable patterned nanoparticle domains for a variety of functional materials and applications.