Atomistic damage near the Si surface by nanoindentation is investigated using atomically flat Si surfaces and ultralow dissolved-oxygen water (LOW) treatment. No characteristic phenomena of plastic deformation such as pop-in or pop-out events are observed in the load-displacement curve during nanoindentation for a maximum load of a few micronewtons by atomic force microscopy (AFM). After nanoindentation on the Si surface, however, the fine vestiges with the dents and swells are observed. This indicates that nanoindentation of just a few micronewtons clearly leaves the plastic deformation near the Si surface. In addition, concentric triangles corresponding to the indentation positions are embossed during immersion in the LOW. The precise observation of these triangular patterns by the AFM indicates that the nanoindentation also generates secondary crystallographic damage under the dents of the primary damage.