Parallel processes for patterning densely packed nanometre-scale structures are critical for many diverse areas of nanotechnology. Thin films of diblock copolymers can self-assemble into ordered periodic structures at the molecular scale (approximately 5 to 50 nm), and have been used as templates to fabricate quantum dots, nanowires, magnetic storage media, nanopores and silicon capacitors. Unfortunately, perfect periodic domain ordering can only be achieved over micrometre-scale areas at best and defects exist at the edges of grain boundaries. These limitations preclude the use of block-copolymer lithography for many advanced applications. Graphoepitaxy, in-plane electric fields, temperature gradients, and directional solidification have also been demonstrated to induce orientation or long-range order with varying degrees of success. Here we demonstrate the integration of thin films of block copolymer with advanced lithographic techniques to induce epitaxial self-assembly of domains. The resulting patterns are defect-free, are oriented and registered with the underlying substrate and can be created over arbitrarily large areas. These structures are determined by the size and quality of the lithographically defined surface pattern rather than by the inherent limitations of the self-assembly process. Our results illustrate how hybrid strategies to nanofabrication allow for molecular level control in existing manufacturing processes.