A significant need in nanotechnology is the development of methods to mass-produce three-dimensional (3D) nanostructures and their ordered assemblies with patterns of functional materials such as metals, ceramics, device grade semiconductors, and polymers. While top-down lithography approaches can enable heterogeneous integration, tunability, and significant material versatility, these methods enable inherently two-dimensional (2D) patterning. Bottom-up approaches enable mass-production of 3D nanostructures and their assemblies but with limited precision, and tunability in surface patterning. Here, we demonstrate a methodology to create Self-folding Nanostructures with Imprint Patterned Surfaces (SNIPS). By a variety of examples, we illustrate that SNIPS, either individually or in ordered arrays, are mass-producible and have significant tunability, material heterogeneity, and patterning precision.