Directed self-assembly (DSA) of block copolymers (BCP) is attracting a growing amount of interest as a technique to expand traditional lithography beyond its current limits. It has recently been demonstrated that chemoepitaxy can be used to successfully direct BCP assembly to form large arrays of high-density features using the ‘LiNe’ flow. This process uses lithography and trim-etch to produce a “prepattern” of stripes of alternating chemical composition, which in turn guide the formation of assembled BCP structures. The entire process is predicated on the preferential interaction of the respective BCP domains with particular regions of the underlying prepattern. The natural and relative strength of these interactions are at least partially responsible for many aspects of the resulting assembled BCP film, including equilibrium morphology, type and persistence of kinetically trapped defects, and domain roughness. This study develops the understanding of how various guiding chemistries ultimately govern BCP morphology and characteristics in the LiNe flow. In particular, the work focuses on how stronger affinity between chemical patterns and the guided BCP film leads to faster assembly, lower ultimate defectivity levels, and better incommensurability tolerance, as well as the relationship between pattern strength and domain roughness. One issue in generating finely controllable chemical patterns is that all materials are affected to some degree by processing, which can modify or weaken the guiding ability of the pattern. This investigation addresses the non-idealities introduced in production processing and explores how this knowledge can be employed in improving BCP DSA for lithography.