This chapter is focused on the use of ion-beam processing for controlling the linear and nonlinear optical properties of different nanostructures based on metallic clusters embedded in silica. Three case studies will be presented: the first is the modification of the surface-plasmon resonance of metallic nanoclusters by direct implantation or irradiation. The second is the far-field and local-field modification by means of controlled ion irradiation of bimetallic nanoclusters. The last example deals with the synthesis of ordered plasmonic nanostructures using ion implantation and/or irradiation. These three examples are a sort of hierarchical approach to the control of the optical properties of nanostructures based on nanoparticles, starting from the synthesis of the functional building block of our approach, i.e., randomly positioned metal nanoparticles in silica, to end at the last level with the formation by ion-implantation-ordered arrays (chains or planar 2D assembly). In all these examples, ion implantation demonstrates to be not only a simple synthesis technique, but a very powerful processing tool for obtaining new functional properties. A brief description of the theoretical approach to the comprehension of the light-particle interaction from a semiclassical point of view will be given to aid the interpretation of the experimental results.