This work presents the application of the Quasicontinuum Method (2-dimensional) initially developed by Tadmor et al (1996 Phil. Mag. 73 1529) to an indentation process taking account of the atomic structure of both the indenter and substrate subject to indentation. Aspects relating to slip planes, dislocation nucleation and nanostructure formation are presented for different indenter materials (Ag, Cu and Pd) and indenter crystal orientations. Slip vectors near to the indenter contact region show that depending on the material and orientation of the indenter the plastic deformations occur either inside the indenter or the substrate. Long-range material deformations appear during the indentation or retraction of the indenter. All of these aspects mainly dictate the formation of nanoclusters or nanoholes on the substrate surface.
