Molecular dynamics simulations are used to investigate how the nanoimprint lithography mechanism influences the filling interaction and mechanical deformation on polymethylmethacrylate (PMMA) surfaces. The effects of two mold geometries and various taper angles were investigated using stress, slip vector, molecular trajectories, and applied force analysis. For the PMMA formation mechanism on a concave-like mold imprint, the molecules were extruded upward into the mold space after the molecules on two sides were downward compressed by the mold. The formation mechanism is opposite to that for the tip-like mold imprint because the molecules are firstly compressed downward by the tip. The results show that the slowest filled areas of the pattern were at the two corners of the tip where stress value was low. The filling speed in both the tip-like mold and the concave-like mold imprint increased with the taper angle increased due to filling space and smaller capillary flow. Due to the effect of capillary flow, the concave-like mold needs much more loading force to transfer the pattern than the tip-like mold. The loading force and curve oscillation increased with the taper angle in the tip-like mold imprint, but they significantly increased with decreasing taper angle in the concave-like mold. The high stress was mainly concentrated on the molecules near the tip and underneath the mold for the tip-like mold and the concave-like mold imprint, respectively. The relationship of the magnitude of taper angle to the loading force is similar to stress and slip vector.