Single panel processing of polymeric microfluidic devices has been widely researched in recent years. However, suitable high throughput roll-to-roll replication methods are still limited. Taking cue from the conventional hot embossing process and roll-to-roll web processing methods, a hot roller embossing machine for fabricating polymeric microfluidic devices was built. This paper discusses the effects of process parameters such as embossing pressure, substrate preheating, roller temperature and roller speed on the embossed channel depth. In addition, mold channel orientation and pattern density effects were also highlighted as crucial factors that could affect the fidelity of pattern transfer. The above parameters and factors were explored with the goal of achieving process optimization.