In this work the pore filling of nanostructured silicon with metals and especially with magnetic materials is elucidated. A brief overview of often-used templates is given, then the filling processes are discussed. Two approaches are depicted: first, the deposition of magnetic nanostructures out of a metal salt solution, and, second, the infiltration of readily synthesized magnetic nanoparticles, both resulting in a three-dimensional arrangement of metal nanostructures within the porosified layer. The deposition/infiltration and the resulting arrangements of the nanostructures as well as their preferential growth within the pores are discussed. Furthermore, the magnetic properties of the nanocomposite systems with respect to the deposition parameters and also in terms of modification of the porous silicon morphology are investigated. One crucial point is the magnetic interaction between the nanostructures of the arrays, which is elucidated in detail. Thereby the interaction between nanostructures within one pore and the coupling between nanostructures within adjacent pores are considered. In the latter case the interaction mainly depends on the morphology of the template.