A three-dimensional molecular dynamics (MD) model is utilized to investigate the effect of tool geometry on the deformation process of the workpiece and the nature of deformation process at the atomic-scale. Results show that different states exist between the atomic force microscope (AFM) pin tool and the workpiece surface, i.e. the non-wear state, the ploughing state, the state in which ploughing is dominant and the state in which cutting plays a key role. A relationship between the deformation process of the workpiece and the potential energy variation is presented. The potential energy variation of atoms in different deformed regions in the workpiece such as plastically deformed region, elastically deformed region and the mixed deformation region is different. The features of variations of potential energy are discussed. (c) 2005 Elsevier B.V. All rights reserved.