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This research investigates deformation behavior of polystyrene (PS) as a thermoplastic resist material for the thermal nanoimprint lithography (T-NIL) process. Molecular dynamics modeling was conducted on a PS substrate with dimensions 58 × 65 × 61 Å that was imprinted with a rigid, spherical indenter. The effect of indenter size, force, and imprinting duration were evaluated in terms of indentation depth, penetration depth, recovery depth, and recovery percentage of the polymer. The results show that the largest indenter, regardless of force, has the most significant impact on deformation behavior. The 40 Å indenter with a 1 µN of force caused the surface molecules to descend to the lowest point compared to the other indenters. An increase in indenter size resulted in higher penetration depth, recovery depth, and recovery percentage. Higher durations of imprint cycle (400 fs) resulted in plastic deformation of the PS material with minimal recovery (4 Å). The results of this research lay the foundation for explaining the effect of several T-NIL process parameters on virgin PS thermoplastic resist material.