This study aims at investigating the distortion of poly(dimethylsiloxane) (PDMS) nanostructures in a soft lithography demolding process using molecular dynamics simulation. Experimental results show that after peeling, PDMS nanopillars became 10–60% longer in height than the mold size. Molecular dynamics simulations have been employed to plot the stress–strain curve of the nanopillars when subjected to uniaxial stress. Three force fields (COMPASS, CVFF, and PCFF) were used for modeling. The demolding process in soft lithography and nanoimprint lithography causes significant deformation in replication. The experimental results show clear signs of elongation after demolding. Molecular dynamics simulations are employed to study the stress–strain relationship of the PDMS nanopillars. The results from the simulation show that a PDMS nanopillar at temperature T = 300 K under tensile stress shows characteristics of flexible plastic under tensile stress and has a lower Young’s modulus, ultimate tensile stress, and Poisson’s ratio.