The combination of lithographic methods with 2D DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micron scale. Here we extend this concept to the third dimension by mounting 3D DNA origami onto nano-patterned substrates, followed by silicification to provide mechanical and chemical stability. We created fully addressable, three-dimensional nanopatterns of hybrid DNA-silica structures with heights up to 50 nm and feature size in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to 3D-position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and 3D-patterned surfaces and integrated devices designed on the molecular level while reaching macroscopic dimensions.