We demonstrate a method, employing prepatterns based on hydrogen silsesquioxane (HSQ) resist, for fabricating highly dense dot arrays of perpendicular block copolymer (BCP) cylinders with improved quality or increased density multiplication factors compared to conventional SiOx-based chemical prepatterns (dot arrays of exposed SiOx surfaces surrounded by polystyrene (PS) brush matrix). Due to the higher quality and simpler preparation procedures, HSQ-based chemical prepatterns were able to induce better BCP patterns, including nearly perfectly ordered and well registered arrays of perpendicular poly(styrene-b-dimethylsiloxane) (P(S-b-DMS)) cylinders. On prepatterns with identical chemical properties and patterning features, graphoepitaxy can induce higher density multiplication than chemical prepatterning.