The atomic force microscopy (AFM)-based nano lithographic technique is currently used to directly machine material surfaces and fabricate nano components for MEMS (micro electro mechanical system). As such, three-dimensional molecular dynamic computer simulations were conducted to evaluate the characteristics of the nano lithography process. The 3-dimensional molecular dynamic (MD) simulations were carried out on monocrystalline copper by varying specific combinations of the crystal orientation and cutting(plowing) direction to investigate their effect on the nature of the deformation.