Polymer films nanoimprinted with checkerboard patterns of square wells align calamitic (rodlike) liquid crystals vertically, horizontally, or tilted depending on the depth/width ratio of the wells. The liquid crystal prefers planar orientation on polymer films that are smooth but when the films are topographically patterned, the increasing elastic energy density as the wells become narrower eventually overcomes the surface anchoring of the polymer and the liquid crystal director field makes a transition from planar to homeotropic. Similar effects have been demonstrated in both nematics and smectics, and the behavior is confirmed by theory and computer simulation.