In this paper, we investigate the directed self-assembly of block copolymers in topographical guiding patternswith feature sizes in the range of the block copolymer half-pitch. In particular, we present the selfassemblyof an 11.7 nm half-pitch block copolymer in sub-10 nm resolution guiding patterns fabricated bythe direct e-beam exposure of hydrogen silsesquioxane (HSQ). One result of this analysis is that the blockcopolymer self-assembles such that the guiding pattern features form part of the 3-D architecture of thefilm. We are capable of determining a shift in the block copolymer pitch as a function of the guiding patternpitch with sub-nanometer accuracy by means of both real-space (AFM, SEM) and reciprocal-spacetechniques (GISAXS). An interesting result is that the block copolymer self-assembly in the studied structuresdepends 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 experimentalevidence of a narrower processing window for such kind of guiding patterns than for regular directed selfassemblyusing wide topographical guiding patterns, and discuss the origin of this effect. We argue thatchain deformation in the vicinity of the top cap of the guiding pattern feature is responsible for an increaseof the free energy of the ordered state, which leads to a smaller energy difference between the defect-freeand defective self-assembly than that for the observed self-assembly morphology.