In this study, latent and etched ion tracks generated by high electronic excitation in alpha quartz (α-SiO2) were characterized. Single crystals of Y- and Z-cut α-SiO2 were irradiated at room temperature with 20 MeV Ni6+ ions and 40 MeV I7+ ions. The track morphology depends on the energy of the incident ion and the stopping power on the target material. Subsequent chemical vapor-etching with hydrofluoric acid solutions was conducted with varying etching times and acid concentrations. The vapor etching process produced nanostructures whose dimensions increased with etching time and etchant concentrations. Y-cut samples etched more slowly than Z-cut samples and exhibited anisotropic track etching behavior. Production of nanowells with different aspect ratios was accomplished by altering the etching time and etchant concentration. The nanowells were characterized by Atomic Force Microscopy. The etched nanostructure templates could be used in the fabrication of novel nanodevices with unique optical, thermal, and electronic properties.