We report a significant role of side chains in the propagation of molecular orientation upon annealing the liquid crystal phase of polyfluorenes. Direct rubbing of poly(9,9-di(octyl)fluorene) led to the orientation of polymer segments in the top-most region of the film and enhanced propagation of this orientation along the rubbing direction was observed upon annealing. In contrast, the rubbing-induced molecular orientation of poly(9,9-di(ethylhexyl)fluorene) segments completely disappeared upon annealing in the nematic melt state. The higher order of the side chain structures in poly(9,9-di(octyl)fluorene) were found to allow the propagation of the three-dimensional molecular alignment. From integrated experimental and density functional theory studies, we propose that side chain interdigitation generates a unique alignment behavior of poly(9,9-di(octyl)fluorene).