The molecular arrangement in thin films of poly(9,9-dioctylfluorene) and poly(9,9-dihexylfluorene) deposited on silicon substrates has been investigated with grazing incidence X-ray diffraction. In particular, the effect of the interface on the molecular orientation is highlighted. Both materials display a periodicity normal to the surface arising from stacked sheets of fluorene chains in both the crystalline and liquid crystalline phases. For the crystalline phase, a periodicity in the plane of the surface of 4.15 Angstrom is observed corresponding to half the fluorene ring repeat distance along the backbone, consistent with interdigitating side-chains. For crystalline films deposited onto rubbed polyimide films, strong orientation effects are observed. In the liquid-crystalline phase, this strong in-plane ordering of backbones is lost. Poly(9,9-dihexylfluorene) exhibits an additional degree of ordering in the plane of the interface, which is likely to arise from hexagonal ordering of the backbone chains.