Thin films of cylinder-forming polystyrene-b-poly(methyl methacrylate) block copolymer (PS-b-PMMA) were self-assembled on two sets of surfaces homogeneously covered with random copolymer brush composed of PS and PMMA (P(S-r-MMA)), having styrene fractions, F(SV), ranging from 0.57 to 1.0: one set that had been exposed to the lithographic materials and processes without having been patterned and one set that had not. The resulting self-assembled morphologies revealed that the lithographic process shifted the nonpreferential composition of the P(S-r-MMA) brush from F(St) similar to 0.70 to F(St) similar to 0.79. PS-b-PMMA films were then directed to assemble with density multiplication on chemical patterns made from P(S-r-MMA), in which the surface chemistry of the background region of the pattern after lithography ranged from weakly PMMA-preferential (WMP, F(St), = 0.70) to nonpreferential (NP, F(St), = 0.79) to weakly PS-preferential (WSP, F(St) = 1.00). The extent of density multiplication ranged from 1:1 to 16:1. The assemblies were analyzed in terms of defect quantity and cylinder diameter uniformity, as observed by top-down scanning electron microscopy (SEM). In general, many fewer defects were observed for the assemblies on the WSP chemical pattern than on the WMP chemical pattern. The best assemblies occurred on the NP chemical patterns, with no defects apparent in the SEM images of assemblies with up to 4:1 density multiplication and with spot size variation sufficiently low for bit patterned media applications. As the extent of density multiplication was increased (6:1, 9:1, and 16:1), the defect density monotonically increased.