Metals of hybrid nano-/microstructures are of broad technological and fundamental interests. Manipulation of shape and composition on the nanoscale, however, is challenging, especially for multicomponent alloys such as metallic glasses. Although top-down approaches have demonstrated nanomoulding, they are limited to very few alloy systems. Here we report a facile method to synthesize metallic glass nanoarchitectures that can be applied to a broad range of glass-forming alloys. This strategy, using multitarget carousel oblique angle deposition, offers the opportunity to achieve control over size, shape and composition of complex alloys at the nanoscale. As a consequence, nanostructures of programmable three-dimensional shapes and tunable compositions are realized on wafer scale for metallic glasses including the marginal glass formers. Realizing nanostructures in a wide compositional range allows chemistry optimization for technological usage of metallic glass nanostructures, and also enables the fundamental study on size, composition and fabrication dependences of metallic glass properties.