Mechanical instabilities such as buckling, wrinkling, creasing, and folding are commonplace in both natural and synthetic systems over a wide range of length scales. In this study, we focus on the spontaneous folding behavior of the highly swellable confined nanoscale (thickness below 100 nm) gel films resulting in the formation of a network of regularly folded structures spontaneously emerging in the course of their swelling and drying. We suggest that regular self-folding is originated from periodic instabilities (wrinkles) caused by swelling-initiated stresses under confined conditions. Furthermore, folded gel structures can be organized into regular serpentine-like manner by imposing various boundary conditions on microimprinted surfaces. We suggest that this demonstration of uniform gel to mechanically mediate morphogenesis has far-reaching implications in the creation of complex, large-area, 3D gel nanostructures.