The filling efficiency during the hot embossing process at micro scale is essential for micro-component replication. The presence of the unfilled area is often due to the inadequate behavior law applied to the embossed materials. This research consists of the identification of viscoplastic law (two-layer viscoplastic model) of polymers and the optimization of processing parameters. Mechanical tests have been performed for two polymers at 20 °C and 30 °C above their glass transition temperature. The viscoplastic parameters are characterized based on stress–strain curves from the compression tests. The influences of imposed displacement, temperature, and friction on mold filling are investigated. The processing parameters are optimized to achieving the complete filling of micro cavities. The replication of a micro-structured cavity has been effectuated using this process and the experimental observations validate the results in the simulation, which confirms the efficiency of the proposed numerical approach.