Reanodizing metal underlayers through porous anodic alumina has already been used extensively to fabricate ordered columns of different metal oxides. Here, we present similar 3D multilayered nanostructures with unprecedented complexity. Two-level 3D column-like nanofilms have been synthesized by anodizing an Al/Nb metal layer in aqueous oxalic acid for forming the first level, and an Al/Ta layer in aqueous tartaric acid for forming the second level of the structure. Both levels were then reanodized in aqueous boric acid. The Ta layer deposited on partially dissolved porous anodic alumina of the first level, with protruding tops of niobia columns, acquired a unique hexagonally-packed structure. The morphology of the first and second levels was determined using scanning electron microscopy. Prolonged etching for 24 h in a 50%wt aqueous phosphoric acid was used to remove the porous anodic alumina. The formation mechanism of aluminum phosphates on the second-level columns in the process of long-time cold etching is considered. The model for the growth of columns on a Ta hexagonally-packed structure of the second level is proposed and described. The described approach can be applied to create 3D two- or three-level column-like systems from various valve metals (Ta, Nb, W, Hf, V, Ti), their combinations and alloys, with adjustable column sizes and scaling. The results of optical simulation show a high sensitivity of two-level column-like 3D nanofilms to biomedical objects and liquids. Among potential applications of these two-level column-like 3D nanofilms are photonic crystals for full-color displays, chemical sensors and biosensor, solar cells and thermoresponsive shape memory polymers.