A method for single-step fabrication of arbitrary, complex, three-dimensional (3D) silicon structures from the nano- to millimeter-scale at multiple levels on non-planar, curved, or domed surfaces is reported. The fabrication is based on focused or masked ion beam irradiation of p-type silicon followed by electrochemical anodization. The process allows fabrication of a wide range of surface features at multiple heights and with arbitrary orientations by varying the irradiated feature width, ion type, energy fluence, and subsequent anodization conditions. The technology has achieved depth resolution of 10 nm as step heights and is capable of creating lateral features down to 7 nm at high aspect ratios of up to 40, with surface roughness down to 1 nm scaled up to full wafer areas. The single-step ability has seamlessly interfaced a network of complex, integrated micro- to nano-structures in 3D orientations with no alignment required. The final template has been converted to a master copy for nano-imprinting lithography of 3D fluidic structures and optical components.