The thermal imprint process of polymer micro-patterning is widely applied in areas such as manufacturing of optical parts, solar energy, bio-mechanical devices and chemical chips. Polycarbonate (PC), as an amorphous polymer, is often used in thermoforming processes because of its good replication characteristics. In order to obtain replicas of the best quality, the imprint parameters (e.g., pressure, temperature, time, etc.) must be determined. Therefore finite element model of the hot imprint process of lamellar periodical microstructure into PC has been created using COMSOL Multiphysics. The mathematical model of the hot imprint process includes three steps: heating, imprinting and demolding. The material properties of amorphous PC strongly depend on the imprint temperature and loading pressure. Polycarbonate was modelled as an elasto-plastic material, since it was analyzed below the glass transition temperature. The hot imprint model was solved using the heat transfer and the solid stress-strain application modes with thermal contact problem between the mold and polycarbonate. It was used for the evaluation of temperature and stress distributions in the polycarbonate during the hot imprint process. The quality of the replica, by means of lands filling ratio, was determined as well.