The development of highly ordered and self-assembled magnetic nanostructures such as arrays of Fe or Ni nanowires and their alloys is arousing increasing interest due to the peculiar magnetic properties of such materials at the nanoscale. These nanostructures can be fabricated using nanoporous anodic alumina membranes or self-assembled nanotubular titanium dioxide as templates. The chemical characterization of the nanostructured layers is of great importance to assist the optimization of the filling procedure or to determine their manufacturing quality. Radiofrequency glow discharge (RF-GD) coupled to optical emission spectrometry (OES) is a powerful tool for the direct analysis of either conducting or insulating materials and to carry out depth profile analysis of thin layers by multi-matrix calibration procedures. Thus, the capability of RF-GD-OES is investigated here for the in-depth quantitative analysis of self-aligned titania nanotubes and self-ordered nanoporous alumina filled with arrays of metallic and magnetic nanowires obtained using the template-assisted filling method. The samples analysed in this work consisted of arrays of Ni nanowires with different lengths (from 1.2 up to 5 microm) and multilayer nanowires of alternating layers with different thicknesses (of 1-2 microm) of Ni and Au, or Au and FeNi alloy, deposited inside the alumina and titania membranes. Results, compared with other techniques such as scanning electron microscopy and energy-dispersive X-ray spectroscopy, show that the RF-GD-OES surface analysis technique proves to be adequate and promising for this challenging application.