Diblock copolymers are self-assembling materials consisting of two polymer chains connected at one end that tend to form ordered nanostructures, including spheres, cylinders, and lamellae, whose shape and dimensions depend on the molecular weight and composition of the polymer. Block copolymer lithography refers to the use of these ordered structures in the form of thin films as templates for patterning through selective etching or deposition. Already block copolymer lithography has been used to pattern dense periodic arrays for the applications such as quantum dots, nanowires, magnetic storage media, increased capacitance gate devices and FLASH memory. One of the current goals in block copolymer nanolithography is to reproduce many of the characteristics of the lithographic process used ubiquitously in nanomanufacturing, including pattern perfection over macroscopic areas, the ability to pattern arbitrary and non-regular geometries, dimensional control of features within exacting tolerances and margins, and registration and overlay. Two strategies will be discussed to integrate self-assembling materials into existing manufacturing practices so as to achieve molecular-level process control and the ability to produce useful architectures: directed assembly of block copolymers on topographically patterned substrates, and directed assembly of block copolymers on chemically nanopatterned substrates.