Various defect structures in a symmetric block copolymer self-assembled in thin films on neutral homogeneous and chemically nanopatterned surfaces were investigated. On neutral homogeneous surfaces, a lamellar morphology lacking long-range order was observed with a high density of defects such as dislocations and disclinations in the two-dimensional plane of the film. On chemically patterned surfaces, the commensurability between the periodicity of the surface pattern and the block copolymer lamellae determined the final structure. When the surface pattern period was commensurate with the natural lamellar period, well-registered defect-free lamellar structures were obtained. In contrast, if the length scales were incommensurate, the formation of new structures such as dislocation dipoles, undulated lamellae, and tilted lamellae was observed. Our present work provides a detailed analysis of these new defect structures. In particular, a model describing the three-dimensional structure of the undulated morphology is suggested.