We describe molecular-scale soft nanoimprint lithographic replication of rubbed polyimide substrates to form alignment layers for liquid crystal devices. Systematic studies of the surface relief morphology of the polyimide and molded structures in three different polymers illustrate good lithographic fidelity down to relief heights of several nanometers, and with some capabilities at the level of approximately 1 nm. Collective results of experiments with several polymer formulations for molds and molded materials and process conditions indicate that this molecular-scale fidelity in replication can be used to produce surfaces that will effectively align liquid crystal molecules. Good electro-optical responses from liquid crystal light modulators that are formed in this manner suggest utility for fundamental studies and potential practical application.