Lamellae forming diblock copolymer domains can be directed to assemble without defects and in registration with chemically nanopatterned substrates. Initially, thin films of the lamellar poly(styrene-b-methyl methacrylate) block copolymer form hexagonally close-packed styrene domains when annealed on chemical nanopatterned striped surfaces. These styrene domains then coalesce to form linear styrene domains that are not fully registered with the underlying chemical surface pattern. Defects coarsen, until defect-free directed assembly is obtained, by breaking linear styrene domains and reforming new structures until registered lamellae have been formed. At all stages in the process, two factors play an important role in the observed degree of registration of the block copolymer domains as a function of annealing time: the interfacial energy between the blocks of the copolymer and the chemically nanopatterned substrate and the commensurability of the bulk repeat period of the block copolymer and the substrate pattern period. Insight into the time-dependent three-dimensional behavior of the block copolymer structures is gained from single chain in mean field simulations. (c) 2005 Wiley Periodicals, Inc.