Focused ion beam (FIB) induced damage in nanocrystalline Al thin films has been characterized using advanced transmission electron microscopy techniques. Electron tomography was used to analyze the three-dimensional distribution of point defect clusters induced by FIB milling, as well as their interaction with preexisting dislocations generated by internal stresses in the Al films. The atomic structure of interstitial Frank loops induced by irradiation, as well as the core structure of Frank dislocations, has been resolved with aberration-corrected high-resolution annular dark-field scanning TEM. The combination of both techniques constitutes a powerful tool for the study of the intrinsic structural properties of point defect clusters as well as the interaction of these defects with preexisting or deformation dislocations in irradiated bulk or nanostructured materials.