The role of anchoring the mesogenic side chains at the internal and boundary interfaces in the thin film morphology has been investigated for two fluorinated side-chain liquid crystalline/amorphous diblock copolymers. Initial bulk investigations indicate that the two polymers strongly microphase segregate into a cylindrical and a lamellar morphology, respectively. Inside the liquid-crystal block, the cylinder-forming block copolymer shows both a crystalline-B and a smectic-A phase, whereas the lamellae-forming polymer gives only a smectic-A phase, with the side chains organized in double layers with a spacing of 3.33 nm. In both situations the smectic layers are oriented perpendicular to the block interfaces, which state is retained in films. In thin films of the cylinder-forming block copolymer, the smectic layering and the orientational wetting properties of the fluorinated side chains stabilize the minority cylindrical domains normal to the substrate. For films of the lamellar system, however, an evolved structure forms with block lamellae parallel to the substrate in combination with anchoring of the fluorinated chains at the surface of the film.