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Understanding the deformation behavior during nanoimprint lithography is crucial for high resolution patterning. Molecular dynamics modeling was implemented to investigate the effect of different mold profiles (cylindrical, rectangular, and spherical) on the von Mises stress, lattice dislocations, and material deformation. Relatively higher von Mises stress (1.08 × 107 Pa) was observed for the spherical mold profile compared to the rectangular and cylindrical profiles due to the larger surface area of contact during the mold penetration stage of NIL. Substantial increases in the von Mises stress were observed for all the mold geometries during the mold penetration stage. The von Mises stresses had a reduction in the relaxation and mold retrieval stages based on the rearrangement of the gold atoms. The lattice dislocation during the deformation process revealed the formation of the BCC structure which further reverted to the FCC structure after the mold retrieval. The polyhedral template matching (PTM) method was used to explain the retention of the FCC structure and subsequent ductile behavior of the substrate. The cylindrical mold had the lowest percentage spring back in both of the orthogonal directions and thus replicated the mold profile with high-fidelity as compared to the spherical and rectangular molds. The findings of this research can aid the design of molds for several applications.