In the framework of swift heavy ion - matter interaction, the thermal spike has proved its worth since nearly two decades. This paper deals with the necessary refinement of the computation due to the kind of materials involved i.e. nanomaterials such
as multilayered systems or composite films constitued of nanocylinders or nanospheres embedded in matrix. The three dimensional computation of the thermal spike model is applied for the first time in layers containing spherical nanoparticles embedded in a silica matrix. The temperature profile calculated at each point (x,y,z) of the target for times up to $10^{-10}$s allows a possible explanation of the particle shape change under irradiation with swift heavy ions having an energy of several MeV/u.m.a. The comparison made with the former 2D version of the code applied to cylindrical gold nanoparticles confirms the validity of the present 3D version.
