Block copolymer thin films provide an attractive method for nanopatterning at size scales inaccessible to conventional photolithographic techniques.1 Block copolymers can microphase separate to form dense, periodic microdomains on the size scale of 10-100 nm.2 To serve effectively as templates, however, the need to impart well-defined positional and orientational order to these microdomains is paramount. One method to achieve long-range orientational order in block copolymer thin films is through the use of shear, which has previously been shown to preferentially orient the microdomains of certain sphere-3, cylinder-4, and lamellae-forming5 systems in the direction of applied shear. Numerous experimental factors influence the ease with which orientation is achieved as well as the ultimate quality of alignment observed. The present work aims to investigate several of these factors by studying the thin film morphology, in both the unaligned (thermally annealed) and shear-aligned states, of cylinder-forming poly(styrene)- poly(n-hexylmethacrylate) (PS-PHMA) copolymers which are of interest for nanolithographic applications such as the production of nanowire polarizing grids for deep ultraviolet light.6 The tendency of PS-PHMA diblocks not to terrace (form "islands" or "holes") at reasonable annealing conditions, but instead to form mixed morphological patterns (mixtures of in-plane and out-of-plane cylinders or spheres) without discrete variation in film thickness makes it challenging to identify the precise monolayer film thickness at which maximum alignment quality is expected to occur. Furthermore, we investigate the effect of block copolymer composition on these thickness dependencies; in particular, we expect that moving the polymer more firmly into the cylinder-forming phase space might reduce the ability of the microdomains to restructure into spheres, and thus dampen the degree to which orientational switching between inplane and out-of-plane cylinders is possible. Once the optimal integer layer film thicknesses are identified we subsequently examine both the limitations to the maximum achievable alignment quality as well as the ease with which these systems are aligned (by looking at alignment quality as a function of applied shear).