Surface alignment and control of hexagonal molecular cylinders from an asymmetric supramolecular liquid crystal was established. Transmission electron microscopy images show that the cylinders are strongly affected by the substrate and film thickness. The cylinders align perpendicular to a hydrophobic substrate, while planar alignment takes place on hydrophilic surfaces. Different morphologies are encountered depending on the film thickness. Thick films of such a material exhibit a highly ordered hexagonal structure where the cylinders are oriented either parallel or perpendicular depending on the substrate. For thin films whose thickness is 10 nm < t < 20 nm, they spontaneously form holes with straight edges aligned with hexagonal symmetry of the (10) orientation of the underlying molecular lattice. Thinner films lead to a liquid-like disordered in-plane structure. Unlike the behaviour of thin films of a typical block copolymer, where the natural period of the block copolymer is manifested through the formation of hole, the hole structures from these types of asymmetric dendrimers can be attributed to the low surface energy planes, revealed by the faceting of discontinuous films.