Many conventional micropatterning and nano-patterning techniques employ toxic chemicals, rendering them nonbiocompatible and unsuited for biodevice production. Herein the formation of water bridges on the surface of hyaluronic acid (HA) films is exploited to develop a transfer-based nanopatterning method applicable to diverse structures and materials. The HA film surface, made deformable via water bridge generation, is brought into contact with a functional material and subjected to thermal treatment, which results in film shrinkage, allowing a robust pattern transfer. The proposed biocompatible method, which avoids the use of extra chemicals, enables the transfer of nanoscale, microscale, and thin-film structures as well as functional materials such as metals and metal oxides. A nanopatterned HA film is transferred onto a moisture-containing contact lens to fabricate smart contact lenses with unique optical characteristics of rationally designed optical nanopatterns. These lenses demonstrated binocular parallax-induced stereoscopy via nanoline array polarization and acted as cutoff filters, with nanodot arrays, capable of treating Irlen syndrome.