Material deformation during nanoimprinting of aluminum (Al), copper (Cu), and gold (Au) was explored through molecular dynamics simulations. A comparative understanding of the deformation behavior of three substrate materials important for design and high-resolution pattern transfer was highlighted. In this study, we analyzed three metrics, including von Mises stresses, lattice deformation, and spring-back for the chosen materials. Of the three materials, the highest average von Mises stress of 7.80 MPa was recorded for copper, while the lowest value of 4.68 MPa was computed for the gold substrate. Relatively higher von Mises stress was observed for all three materials during the mold penetration stages; however, there was a significant reduction during the mold relaxation and retrieval stages. The Polyhedral Template Matching (PTM) method was adopted for studying the lattice dislocation of the materials. Predominantly Body-Centered Cubic (BCC) structures were observed during the deformation process and the materials regained more than 50% of their original Face-Centered Cubic (FCC) structures after mold retrieval. Gold had the lowest vertical spring-back at 6.54%, whereas aluminum had the highest average spring-back at 24.5%. Of the three materials, aluminum had the lowest imprint quality due to its irregular imprint geometry and low indentation depth after the NIL process. The findings of this research lay a foundation for the design and manufacture of Nanoimprint Lithography (NIL) molds for different applications while ensuring that the replicated structures meet the desired specifications and quality standards.