An accurate characterization of subsurface properties is essential to understand machining induced surface integrity. However, little research has been conducted to investigate significant influences of surface integrity (hardness and residual stress) and tip geometry on the indentation process and the resulting load–depth curves. Nanoindentation was used to measure hardness and modulus in the subsurface of machined components by turning, grinding, and honing. The machining induced residual stresses can be estimated by matching the FEA simulated load–depth curves with the experimental ones. The simulation sensitivity analysis shows that the load–depth curves are significantly affected by residual stress and modulus, while friction, tip rounding, and yield strength have much smaller effects. The peak normal stresses occur on the top surface, while the peak shear stress is slightly under the surface. All peak strains are in the subsurface. The onset of material yielding during loading may be determined by tracing the evolution of loading/unloading loops at different indentation depths. A 3D simulation of nanoindentation with a spherical tip has shown that the indentation force induced by the spherical tip is less than 2% of the total force provided that the indentation depth is sufficiently large.