The Letter concerns surface nanodeformation of Si crystal using atomistic simulation. Our results account for both the occurrence and absence of pop-in events during nanoindentation. We have identified two distinct processes responsible for indentation deformation based on load-depth response, stress-induced evolution of crystalline structure and surface profile. The first, resulting in a pop-in, consists of the extrusion of the crystalline high pressure Si-III/XII phase, while the second, without a pop-in, relies on a flow of amorphized Si to the crystal surface. Of particular interest to silicon technology will be our clarification of the interplay among amorphization, crystal-to-crystal transition, and extrusion of transformed material to the surface.