The uniaxial chain alignment of low molecular weight poly(9,9-bis(ethylhexyl)fluorene-2,7-diyl) (PF2/6) in thin films cast atop rubbed polyimide templates is characterized by polarized optical absorption spectroscopy, carbon K near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and grazing incidence X-ray diffraction (GIXRD) in response to thermal annealing and increasing film thickness (ca. 15-150 nm). The highest overall levels of uniaxial alignment are obtained in the thinnest PF2/6 films. However, the orientation of chains at the top surface after thermal annealing is nearly thickness independent despite a large drop in the maximum optical dichroic ratio as the film thickness increases. The kinetics of chain alignment on heating are strongly film thickness dependent and only weakly correlated with a crossover to a nematic liquid crystal state. All told these data support a structural model in which there is a graded morphology such that the top and bottom surfaces exhibit appreciable planar, uniaxial alignment while the film interior includes a greater proportion of nomplanar (i.e., tilted) chains after thermal cycling. These inhomogeneities are likely to influence technologically important optical and transport properties.