Molecular dynamics (MD) simulations have been carried out in order to investigate morphological changes in three different crystallographically oriented silicon surfaces during nanoindentation. Transformations to fivefold and sixfold coordinated structures are observed during the contact loading. However, the atoms are arranged in a complex mix of different local structures rather than forming a new crystalline phase. This region forms a thin layer of around 15 Å under the contact area. The thermal vibration of the atoms is found to have an important role in the recovery of the damage region during tip retraction.