A complex prepolymerized film comprising monomers, cross-linkers, and initiator is usually used to create molecularly imprinted polymers. We herein exploit ready-to-use resist materials and link molecular surface imprinting with UV- and thermo-nanoimprinting techniques to create a sensor layer for the specific recognition of the bacterial surface markers lipopolysaccharide (LPS) and lipoteichoic acid (LTA). To account for the highly polar moieties of LPS and LTA, we evaluate different resist and stamp materials of distinct surface properties by AFM and molecularly imprinted sorbent assays. Thermo nanoimprinting of LPS and LTA micelles to Epon 1002F films exhibits excellent sensitivity of up to 13 times increased signals compared to those of the nonimprinted films and negligible cross-reaction with the tested nonspecific analyte. Additionally, the sensitivity and selectivity of the thermo nanoimprints is compared to conventional molecular surface imprints using a cocktail of acrylic monomers in QCM measurements.