The thermo-mechanical analysis and the mechanical design of the accelerator of MITICA (i.e. the full size prototype of the ITER neutral beam injector under construction at RFX [1]) are based on the calculation of the power deposition induced by particle impacts. This calculation is performed by EAMCC [2], a relativistic particle tracking code based on the Monte-Carlo method for describing collisions inside the accelerator, under prescribed electric and magnetic fields. The magnetic field maps are produced by 3D codes, while the electric field maps come from the 2D axi-symmetric code SLACCAD [3]. In order to perform a multi-beamlet analysis, which allows to take into account the beamlet-beamlet repulsion, and to consider other effects neglected under the hypothesis of axi-symmetric beam, a fully 3D version of the code is required. In this paper, a modified version of EAMCC, fully 3D, capable of modifying the mesh of the 3D maps and of dealing with uneven meshes is presented. A finer mesh is used just in the regions where a more detailed description of the fields is required, for a more realistic simulation. A comparison between the original code and the modified version is presented at first, as a validation of the modifications introduced in the latter. Subsequently, the main results of a single-beamlet analysis performed with the two versions of the code are shown and the differences between the 2D and the 3D simulations discussed. The last part is dedicated to the multi-beamlet simulation of the accelerator.