Poly(alkoxyphenylenevinylene-b-isoprene) (PPV-b-PI) rod-coil block copolymers demonstrate novel structures due to the rodlike PPV block. Thin films of the polymers self-assemble into lamellar microphases upon thermal annealing with the lamellae oriented primarily parallel to the substrate. The parallel lamellae show symmetric wetting of PI at both the substrate and vacuum interfaces. Grains of lamellae with parallel orientation are characterized by irregular polygon shapes and are bounded by defect regions where the lamellae are oriented out of the plane of the film. Grazing-incidence small-angle X-ray scattering (GISAXS) shows that these out-of-plane lamellae are strongly oriented perpendicular to the film. The perpendicular lamellae are much straighter than those typically observed in coil-coil block copolymers due to the high bending energy of the liquid crystalline rod nanodomains. Islands or holes form in the films, and domain spacings estimated from the island/hole heights are equal to the bulk domain spacing. The perpendicular "defect" lamellae mediate the change in thickness required to transition between islands or holes and the surrounding region. Increasing film thickness results in an increasing fraction of the surface covered by perpendicular lamellae, presumably due to limited penetration of the substrate orienting field into the film. At great enough thickness total reorientation of the lamellar structure from parallel to perpendicular orientation at the vacuum interface is observed.