We present experimental results and numerical Finite Element analysis to describe surface swelling due to the creation of buried graphite-like inclusions in diamond substrates subjected to MeV ion implantation. Numerical predictions are compared to experimental data for MeV proton and helium implantations, performed with scanning ion microbeams. Swelling values are measured with white light interferometric profilometry in both cases. Simulations are based on a model which accounts for the through-the-thickness variation of mechanical parameters in the material, as a function of ion type, fluence and energy. Surface deformation profiles and internal stress distributions are analyzed and numerical results are seen to adequately fit experimental data. Results allow us to draw conclusions on structural damage mechanisms in diamond for different MeV ion implantations.