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In this paper it is demonstrated how nanoindentation can be used to assess the subsurface damage induced by nanomachining. To accomplish this, a characteristic difference in the nanoindentation response between plastically deformed and undeformed material is exploited. Classical molecular dynamics simulations are performed to investigate the elementary mechanisms of the irreversible plastic processes that occur during nanomachining of a copper single crystal. To mimic the experimental characterization of subsurface damage, we perform nanoindentation simulations into the machined surface. The results show that the critical contact pressure required for dislocation nucleation, i.e. the pop-in load, decreases continuously with increasing machining depth, while the indentation hardness seems widely unaffected by prior nanomachining.