The directed self‐assembly of block copolymer (BCP) materials in topographically patterned substrates (i.e., graphoepitaxy) is a potential methodology for the continued scaling of nanoelectronic device technologies. In this Communication, an unusual feature size variation in BCP nanodomains under confinement with graphoepitaxially aligned cylinder‐forming poly(styrene)‐block‐poly(4‐vinylpyridine) (PS‐b‐P4VP) BCP is reported. Graphoepitaxy of PS‐b‐P4VP BCP line patterns (CII) is accomplished via topography in hydrogen silsequioxane (HSQ) modified substrates and solvent vapor annealing (SVA). Interestingly, reduced domain sizes in features close to the HSQ guiding features are observed. The feature size reduction is evident after inclusion of alumina into the P4VP domains followed by pattern transfer to the silicon substrate. It is suggested that this nanodomain size perturbation is due to solvent swelling effects during SVA. It is proposed that using a commensurability value close to the solvent vapor annealed periodicity will alleviate this issue leading to uniform nanofins.