Issues on the superficial oxidation of mesoporous amorphous silicon and germanium photonic layers generated at oblique angles are reported. Such films were designed to improve the transmittance of optical elements over the mid-IR window (3.6-4.9 mu m) by removing the light reflection. These nanostructures were deposited on silicon substrates by e-beam evaporation at room temperature. IR ellipsometry and spectrophotometry studies combined with models based on effective medium approximations predicted the presence of silicon or germanium oxides. Such oxidation was evidenced by combining X-ray photoelectron spectroscopy and advanced (scanning-)transmission electron microscopy studies based on energy-dispersive X-rays and electron energy-loss spectroscopies. Both techniques also allowed to prove the formation of core-shell-type architectures consisting of pure Si or Ge surrounded by oxidized species, even for a Ge layer subsequently capped with a dense MgF2 coating. The different approaches used for preparing electron transparent specimens (tripod polishing and focused ion-beams) confirmed a fast oxidation of the Ge nanocolumns even for short air exposure periods, and allowed comparing it with the level of oxidation promoted from other pollutant sources. This work sheds light on the spontaneous undesired oxidation in Si or Ge slanted nanorods which can diminish the performances and limit further development of optical devices.