The thermal alignment of the liquid crystalline fluorene-thiophene copolymer (F8T2) on rubbed polyimide surfaces is investigated by ex-situ and in-situ X-ray scattering experiments. The ex-situ characterization allows an assignment of the observed diffraction peaks to distances between polymer backbones (1.6 nm), distances between the flexible side groups of the polymer chains (0.43 nm), and intramolecular distances of adjacent ring units (0.5 nm). The in-situ characterization allows a temperature dependent observation of the polymer chain alignment. A gradual alignment process of the polymer backbones is observed for temperatures up to 563 K. Decreasing temperature after the polymer chain alignment is accompanied by a glass transition of the side chains at 380 K. (C) 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1599-1604, 2009