Abstract: Three-dimensional molecular dynamics (MD) simulation was conducted to study the effect of indenter size on the AFM-based nanoindentation process of monocrystalline copper film.The Morse potential was utilized to compute the interaction between workpiece atoms and tool atoms,and also the interaction between sample workpiece atoms.The results show that the plastic deformation via amorphous transformation is the mechanism of nanoindentation of monocrystalline copper film.The MD simulation results of nanoindentation process were significantly affected by the indenter size,indicating the nanoindentation size effect.