Nanometer scale layered systems are well suited to investigate atomic transport processes induced by high-energy electronic excitations in materials, through the characterization of the interface transformation. In this study, we used the atom probe technique to determine the distribution of the different elements in an (amorphous-Fe$_2$Tb 5 nm/hcp-Co 3 nm)$_{20}$ multilayer before and after irradiation with Pb ions in the electronic stopping power regime. Atom probe tomography is based on reconstruction of a small volume of a sharp tip evaporated by field effect. It has unique capabilities to characterize internal interfaces and layer chemistry with sub-nanometer scale resolution in three dimensions. Depth composition profiles and 3D element mapping have been determined, evidencing for asymetric interfaces in the as-deposited sample, and very efficient Fe-Co intermixing after irradiation at the fluence $7\times10^{12}$ ion cm$^{-2}$. Estimation of effective atomic diffusion coefficients after irradiation suggests that mixing results from interdiffusion in a molten track across the interface in agreement with the thermal spike model.