Deformation during spherical and pointed indentation in (100) crystalline silicon usig a UMIS-2000 nanoindenter has been studied using cross-sectional transmission electron microscopy (XTEM), atomic force microscopy (XTEM), atomic force microscopy and Raman microspectroscopy. XTEM samples were prepard by focused ion beam milling to accurately position the cross-section through the indentations. Indentation loads were chosen below an above the yield point for silicon to investigate the modes of plastic deformation. Slip planes are visible in XTEm micrographs for all indentation loads studied but slip is not the main avenue for plastic deformation. A thin layer of poly-crystalline material has been identified (indexed as Si-XII from diffraction patterns) on the low load indentation, just prior to yield (pop-in during loading). For loading above the yield point, a large region of amorphous silicon was observed directly under the indenter when fast unloading conditions were used. The various microstructures and phase observed below indentations are correlated with load/unload data.