The filling of hierarchical branched porous anodic alumina (PAA) templates with magnetic and metallic nanowires using pulsed electrodeposition is here addressed in detail. We show that the electrodeposition potential (and current) reveals clear anomalies when each generation of branched pores created by steady-state or non-steady-state anodisation is completely filled, thus signalising clearly the growth stages. This allowed us to infer that each stage of PAA filling corresponds to a new hierarchical level of the branched structure. We show that the anomalies in the electrodeposition potential (current) were related to the change in porosity, and a linear relation between the electrodeposition potential and the template porosity during metal filling was established. Such a linear relation can be used as a new tool to easily determine the local porosity of anodic metal oxides, independent of the corresponding pore architecture. This work allows one to accomplish a precise control of the nanowires during their growth, opening a path to fill the several hierarchical levels of multiple branched pores with different materials, aiming for the production of multicomponent nanostructures.