Individual authentication using artefact metrics has received increasing attention as a greater importance has been placed on the security of individual information. These artefact metrics must satisfy the requirements of individuality, measurement stability, durability, and clone resistance, in addition to possessing unique physical features. In this study, we proposed that nanostructures of synthetic quartz (SQ) deposited on an SQ plate may provide such sophisticated artefact metrics if morphological changes can be intentionally introduced into the SQ nanostructures at certain positions. We fabricated SQ nanopillars using a mass-production method (namely ultraviolet nanoimprint lithography) and investigated their mechanical deformation using nanoindentation with a spherical diamond tip through loading and unloading cycles. The SQ nanopillars with an aspect ratio of 1 (i.e. diameters D of 100 and 200 nm and heights H of 100 and 200 nm, respectively) could be plastically deformed without collapsing within a specified pillar-array format at programmed positions. The plastically deformed SQ nanopillar arrays demonstrated multi-scale (sub-millimetre, micrometre, and nanometre) and multi-level (shape, area, diameter, and height) individuality authentication and clone resistance capabilities. Because SQ is physically and chemically stable and durable, the individuality authentication will be a highly reliable media on Earth and in space.