In the design and engineering of functional core-shell nanostructures, materials characterization at small length scales remains one of the major challenges. Here we show how electron tomography in high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) mode can be applied successfully to perform nano-metrological characterization of Au@Ag core-shell nanostructures. This work stresses the benefits of HAADF-STEM tomography and its use as a novel and rigorous tool for understanding the physical-chemical properties of complex 3D core-shell nanostructures. The reconstructed Au@Ag core-shell architecture was used as input for Discrete Dipole Approximation (DDA)-based electrodynamics simulations of the optical properties of the nanostructures. The implications for localized surface plasmon spectroscopy as well as in Raman-enhanced spectroscopies are analysed