Nanoindentation is a commonly used method to measure the hardness of surfaces with thin layers, and is especially useful in studying the change in mechanical properties of ion irradiated materials. This research compares two different methods of nanoindentation to study the changes in hardness resulting from ion irradiation of SS316 alloy. The samples were irradiated by He2+ ions at beam energies of 1, 2, and 3 MeV, respectively. The first method involves the indentation of the irradiated surface perpendicular to it using the continuous stiffness mode (CSM), while the second applies the indents on an oblique surface, accessing an inclined cross-section of the irradiated material. Finite element modelling has been used to further illuminate the deformation processes below the indents in the two methods. The hardness profiles obtained from the two nanoindentation methods reveal the differences in the outcomes and advantages of the respective procedures, and provide a useful guideline for their applicability to various experimental conditions. It is shown through an in depth analysis of the results that the ‘top-down’ method is preferable in the case when the ion irradiation energy, or, equivalently, the irradiated depth is small, due to its greater spatial resolution. However, the oblique cross section method is more suitable when the ion irradiation energy is >1 MeV, since it allows a more faithful measurement of hardness as a function of dose, as the plastic field is much smaller and more sensitive to local hardness values.