Molecular dynamics (MD) analysis at the nanometric scale is a powerful tool for understanding the deformation mechanisms of materials when undeformed chip thickness is at atomic or nanometric scale. Until now, two-dimensional and 2.5D MD models have been employed in the MD analysis. With advances in computer performance, it is possible to simulate larger-scale MD in a reasonable time. This article presents a three-dimensional (3D) tool with a cutting-edge radius of 3 nm and a nose radius of 25 nm to reduce computation time. Taper cut is carried out on monocrystalline silicon to verify the model proposed. A smooth surface is achieved before fracture surfaces occur when the depth of cut is below a critical value. The 3D model is also verified by comparing with results obtained by other studies.