In the present study, we aim to investigate the basic flow and filling characteristics in the hot embossing filling stage, which depend on the geometry and processing conditions. For this purpose, we have developed a numerical analysis to simulate hot embossing filling using the finite element method and verified the developed program using the existing experimental data. As s basic study to understand hot embossing filling we have chosen a simple rectangular cavity with repeating protruded parts as a computational domain. The filling pattern was found to be significantly influenced by the variation of thickness of polymer substrate for the same stamp geometry, thermal boundary condition, and the embossing time. Filling from the border of the cavity is clearly observed as the thickness of polymer substrate decreases under the equal wall temperature condition. As for the effect of unequal temperature at the stamp and solid base plate, we found that the filling pattern has been affected by the temperature difference between the two surfaces and embossing time. The localized uprising flow results from the thermal boundary condition and subsequent change in the effective thickness of polymer substrate having enough fluidity to deform.