We demonstrate a soft lithography approach for fabrication of a topographically patterned polyvinyl alcohol (PVA) liquid-crystal (LC) alignment layer. This specific approach employs modified micromolding in capillaries for negative replication of the PVA microstructures on indium tin oxide (ITO) substrates from patterned poly(dimethylsiloxane) molds in a single step, leading to planar alignment on the desired regions. By doping with polyhedral oligomeric silsesquioxane nanoparticles, which can induce vertical alignment on bare ITO surfaces, periodic LC phase gratings based on an alternating vertical-aligned/hybrid-aligned nematic geometry are presented as an application, and a theoretical model was used to simulate and examine the experimental results.