Depth-sensing indentation tests are used to characterize non-conventional materials, such as biomaterials, which normally require particular considerations in terms of specimen preparation. The force-depth measurements during the test reveals valuable information about the material which can be used to obtain the elastic modulus of the sample. Analytical 2D formulas are available in the literature which incorporate a scale factor to establish a proper relationship between the elastic modulus and the force-indentation data. Finite element analysis in 3D was used to simulate the indentation test results, propose a modified scale factor for the analytical solution, and to make a comparison between the modified and original scale factors. The numerical results revealed that the 2D formulation produces closer values to those of the 3D simulations at higher aspect ratios. Additionally, in order to consider the effects of the substrate, two extreme values for the scale factor are proposed.