Nanogranular thin films, in which FePt nannoparticles are dispersed in an amorphous 20 nm thick Al 2 O 3 layer, were irradiated with 2.4 MeV Cu 2þ ions up to 5 Â 10 19 ions/m 2 at room temperature. Electron tomography with a tilt series of bright-field transmission electron microscope images was employed to identify 3-dimensional structural changes due to irradiation. Electron tomography images have clearly revealed that the irradiation with 2.4 MeV Cu 2þ ions causes anisotropic deformation of FePt nanoparticles with elongation along the direction of ions trajectory and slight shrinkage in the perpendicular directions. Ion-irradiation results in disordering in FePt, but post-irradiation annealing at 923 K for 1 h (3.6 ks) leads to re-ordering without significant coarsening and shape change of FePt particles. It has been demonstrated that electron tomography is a quite useful technique for characterization of shape and dispersion of metallic nanoparticles embedded in an amorphous oxide film.