We demonstrate the directional alignment of perpendicular‐lamellae domains in fluorinated three‐armed star block polymer (BP) thin films using solvent vapor annealing with shear stress. The control of orientation and alignment was accomplished without any substrate surface modification. Additionally, three‐armed star poly(methyl methacrylate‐block‐styrene) [PMMA‐PS] and poly(octafluoropentyl methacrylate‐block‐styrene) were compared to their linear analogues to examine the impact of fluorine content and star architecture on self‐assembled BP feature sizes and interdomain density profiles. X‐ray reflectometry results indicated that the star BP molecular architecture increased the effective polymer segregation strength and could possibly facilitate reduced polymer domain spacings, which are useful in next‐generation nanolithographic applications. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 1663–1672