To utilize self-assembled block copolymer structures to fabricate the template of bit patterned media, two basic issues of block copolymer nanodomains need to be considered: (a) size uniformity and (b) position accuracy. The manipulation of domain position was achieved here by graphoepitaxy of cylindrical block copolymer domains in a topographic trench pattern. Trench surface may be neutralized to guarantee the perpendicular orientation of cylindrical domains on the trench bottom surface and domain alignment along the trench sidewall. The size distributions of cylindrical domains on both flat surface and topographically patterned surface have been analyzed and the correlation between the size distribution and the local-range order is addressed. The distributions of the domain size and domain position-related parameters, such as the dot spacing along the axis (parallel to the trench edge) and across the axis, have been investigated as a function of the number of domain rows in the trench. Qualitatively, line edge roughness or linewidth roughness of trenches attributes to the larger variation of spacing across the axis. Finally, a surface trench without neutralization pretreatment was found to enable the graphoepitaxy of block copolymer domains with an areal density >1 Tdot/in.(2). (c) 2007 American Vacuum Society.