We investigate the surface-directed phase separation of spin-coated polystyrene/poly(methyl methacrylate) (PS/PMMA) blends on prepatterned octadecyltrichlorosilane (OTS)-glass substrates under various experimental conditions. As a result of tandem processes of spinodal decomposition and selective wetting of polymer components during spin-coating, low-energy OTS stripes and high-energy glass surfaces laterally arrange the phase-separated polymers according to the chemical pattern on the substrate. Optimal pattern replication was achieved when the length scale of phase separation, controlled via the polymer concentration of the spin-coating solution, matched the smallest feature dimension in a striped chemical pattern possessing two alternating distances between stripes. It was also shown that polymer blend patterns were most closely registered with the underlying substrate when the PS/PMMA composition ratio (30/70, w/w) matched the areal fraction of OTS on the glass surface (similar to 30%). The influence of solvents demonstrated that a solvent with a relatively low volatility, such toluene, was required for patterning so that domain feature sizes were able to coarsen to the size of the patterned features before film vitrification. As well, we showed that the technique and optimized conditions developed in this study could be applied to pattern photoluminescent CdS quantum dots into microscale arrays of parallel lines via spin-coating onto transparent OTS-glass substrates.