Block copolymer (BCP) directed self-assembly (DSA) is an emerging technique, used as an alternative to the traditional photolithography process to obtain ordered patterns with nanoscale dimensions. Following self-assembly, one of the polymer components needs to be selectively removed, to obtain a three-dimensional pattern, which can be transferred onto the semiconductor substrate. This is usually achieved through dry etching, which has been the focus of this thesis. The etching process is difficult to study experimentally, considering the limitations of imaging techniques. Hence, we have developed a coarse-grained model to study the etching of block copolymers (in particular, polystyrene-b-poly (methyl methacrylate) (PS-b-PMMA)), allowing us to study the profile evolution, roughness changes and defect annihilation during the etching process. The parameters allow us to determine the tolerance in the self-assembly process, beyond which the imperfections in the self-assembled morphology will negatively impact further pattern transfer.