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To enable plastic deformation during nanoindentation of an initially defect-free crystal, it is necessary first to produce dislocations. While it is now widely accepted that the nucleation of the first dislocations occurs at the start of the pop-in event frequently observed in experiments, it is unclear how these initial dislocations multiply during the early stages of plastic deformation and produce pop-in displacements that are typically much larger than the magnitude of the Burgers vector. This uncertainty about the complex interplay between dislocation multiplication and strain hardening during nanoindentation makes a direct correlation between force–displacement curves and macroscopic material properties difficult. In this paper, we study the early phase of plastic deformation during nanoindentation with the help of large-scale molecular dynamics simulations. A skeletonization method to simplify defect structures in atomistic simulations enables the direct observation and quantitative analysis of dislocation nucleation and multiplication processes occurring in the bulk as well as at the surface.