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Abstract Sapphire is an attractive material that stands to benefit from surface functionalization effects stemming from micro/nanostructures. Here we investigate the use of ultrafast lasers for fabricating sapphire nanostructures by exploring the relationship between irradiation parameters, morphology change, and selective etching. In this approach a femtosecond laser pulse is focused on the substrate to change the crystalline morphology to amorphous or polycrystalline, which is characterized by examining different vibrational modes using Raman spectroscopy. The irradiated regions are removed using a subsequent hydrofluoric acid etch. Laser confocal measurements quantify the degree of selective etching. The results indicate a threshold laser pulse intensity required for selective etching. This process was used to fabricate hierarchical sapphire nanostructures over large areas with enhanced hydrophobicity, with an apparent contact angle of 140 degrees, and a high roll-off angle, characteristic of the rose petal effect. Additionally, the structures have high broadband diffuse transmittance of up to 81.8% with low loss, with applications in optical diffusers. Our findings provide new insights into the interplay between the light-matter interactions, where Raman shifts associated with different vibrational modes can predict selective etching. These results advance sapphire nanostructure fabrication, with applications in infrared optics, protective windows, and consumer electronics.