We present an effective approach for fabricating nanowell arrays in a one-step laser process with promising applications for the storage and detection of chemical or biological elements. Biocompatible thin films of metallic glasses are manufactured with a selected composition of Zr65Cu35, known to exhibit remarkable mechanical properties and glass forming ability. Dense nanowell arrays spontaneously form in the ultrafast laser irradiation spot with dimensions down to 20 nm. The flared shape observed by transmission electron microscopy is ideal to ensure chemical or biological material immobilization into the nanowells. This also indicates that the localization of the cavitation-induced nanopores can be tuned by the density and size of the initial nanometric interstice from the columnar structure of films deposited by magnetron sputtering. In addition to the topographic functionalization, the laser-irradiated amorphous material exhibits structural changes analyzed by spectroscopic techniques at the nanoscale such as energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy. Results reveal structural changes consisting of nanocrystals of monoclinic zirconia that grow within the amorphous matrix. The mechanism is driven by local oxidation process catalyzed by extreme temperature and pressure conditions estimated by an atomistic simulation of the laser-induced nanowell formation