© 2019 The Royal Society of Chemistry. In this paper, we investigate the directed self-assembly of block copolymers in topographical guiding patterns with feature sizes in the range of the block copolymer half-pitch. In particular, we present the self-assembly of an 11.7 nm half-pitch block copolymer in sub-10 nm resolution guiding patterns fabricated by the direct e-beam exposure of hydrogen silsesquioxane (HSQ). One result of this analysis is that the block copolymer self-assembles such that the guiding pattern features form part of the 3-D architecture of the film. We are capable of determining a shift in the block copolymer pitch as a function of the guiding pattern pitch with sub-nanometer accuracy by means of both real-space (AFM, SEM) and reciprocal-space techniques (GISAXS). An interesting result is that the block copolymer self-assembly in the studied structures depends on the guiding pattern pitch rather than on the trench width as in standard graphoepitaxy. We analyze the structures by means of a free energy model and present both theoretical and experimental evidence of a narrower processing window for such kind of guiding patterns than for regular directed self-assembly using wide topographical guiding patterns, and discuss the origin of this effect. We argue that chain deformation in the vicinity of the top cap of the guiding pattern feature is responsible for an increase of the free energy of the ordered state, which leads to a smaller energy difference between the defect-free and defective self-assembly than that for the observed self-assembly morphology.