A layer-by-layer (LBL) method can generate or approximate any three-dimensional (3D) structure, and has been the approach for the manufacturing of complementary metal-oxide-semiconductor (CMOS) devices. However, its high cost precludes the fabrication of anything other than CMOS-compatible devices, and general 3D nanostructures have been difficult to prototype in academia and small businesses, due to the lack of expensive facility and state-of-the-art tools. It is proposed and demonstrated that a novel process that can rapidly fabricate high-resolution three-dimensional (3D) nanostructures at low cost, without requiring specialized equipment. An individual layer is realized through electron-beam lithography patterning of hydrogen silsesquioxane (HSQ) resist, followed by planarization via spinning SU-8 resist and etch-back. A 4-layer silicon inverse woodpile photonic crystal with a period of 650 nm and a 7-layer HSQ scaffold with a period of 300 nm are demonstrated. This process provides a versatile and accessible solution to the fabrication of highly complex 3D nanostructures.