The geometric structures of the mold and embossing conditions can obviously influence the filling flows in the polymeric patterns. In this study, embossing stamp and substrate with different geometries are used to investigate the flow behavior under both isothermal and non-isothermal conditions. In general, for the stamp, small duty ratio cavity fills more sufficiently than large duty ratio cavity. With the same cavity duty ratio, inner cavity fills more quickly and sufficient than outer cavity. Compared to multiple cavities stamp, individual cavity fills more slowly, especially embossed with the stamp having small duty ratio cavity. Under non-isothermal embossing, the filling flow indicates a wall climbing flow and the polymer flow replaces the outer cavity better. Uncommon substrate provides a limitation of out-squeezing flow from polymer layers, so the polymer pick reaches the mold faster than common substrate like the flat. The present simulation study provides an analysis of the mold geometry especially the substrate geometry to govern filling flow and replication fidelity.