Nanostructured bupivacaine-selective molecularly imprinted 3-aminophenylboronic acid-p-phenylenediamine co-polymer (MIP) films have been prepared on gold-coated quartz (Au/quartz) resonators by electrochemical synthesis under cyclic voltammetric conditions in a liquid crystalline (LC) medium (triton X-100/water). Films prepared in water and in the absence of template were used for control studies. Infrared spectroscopic studies demonstrated comparable chemical compositions for LC and control polymer films. SEM studies revealed that the topologies of the molecularly imprinted polymer films prepared in the LC medium (LC-MIP) exhibit discernible 40 nm thick nano-fiber structures, quite unlike the polymers prepared in the absence of the LC-phase. The sensitivity of the LC-MIP in a quartz crystal microbalance (QCM) sensor platform was 67.6 ± 4.9 Hz/mM under flow injection analysis (FIA) conditions, which was ≈250% higher than for the sensor prepared using the aqueous medium. Detection was possible at 100 nM (30 ng/mL), and discrimination of bupivacaine from closely related structural analogs was readily achieved as reflected in the corresponding stability constants of the MIP-analyte complexes. The facile fabrication and significant enhancement in sensor sensitivity together highlight the potential of this LC-based imprinting strategy for fabrication of polymeric materials with hierarchical architectures, in particular for use in surface-dependent application areas, e.g., biomaterials or sensing.