In this paper, the authors investigated constraints on the quality of topographic features needed for graphoepitaxial assembly of cylinder forming poly(styrene-b-methyl methacrylate) (PS-b-PMMA) thin films, showing the impact of trench width roughness (TWR) on feature size uniformity and defect formation. Topographically patterned substrates were prepared using chemically amplified photoresist and reactive ion etching in conjunction with commercially available lithographic tools and masks. A dose/focus array was utilized to systematically produce trenches with widths between 40 and 400 nm with roughness of 5-35 nm on top of which block copolymers were assembled. Scanning electron microscopy images were taken and analyzed using IMAGEJ software for the metrology of the trenches and ordered block copolymer domains after the removal of the PMMA cylinders. Analysis showed little or no change in domain size variation of the block copolymer with respect to the TWR of lithographically defined features. The impact of TWR on defect formation is qualitatively investigated by classifying all images as having few, some, or many defects. From this analysis, the commensurability between the natural length scale of the block copolymer (l(0)) and the trench width (W) had a significant effect on defectivity, whereas TWR did not play a dominant role.