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.