Three-dimensional magnetic nanostructures hold great potential to revolutionize information technologies and to enable the study of novel physical phenomena. In this work, we describe a hybrid nanofabrication process combining bottom-up 3D nano-printing and top-down thin film deposition, which leads to the fabrication of complex magnetic nanostructures suitable for the study of new 3D magnetic effects. First, a non-magnetic 3D scaffold is nano-printed using Focused Electron Beam Induced Deposition; then a thin film magnetic material is thermally evaporated onto the scaffold, leading to a functional 3D magnetic nanostructure. Scaffold geometries are extended beyond recently developed single-segment geometries by introducing a dual-pitch patterning strategy. Additionally, by tilting the substrate during growth, low-angle segments can be patterned, circumventing a major limitation of this nano-printing process; this is demonstrated by the fabrication of ‘staircase’ nanostructures with segments parallel to the substrate. The suitability of nano-printed scaffolds to support thermally evaporated thin films is discussed, outlining the importance of including supporting pillars to prevent deformation during the evaporation process. Employing this set of methods, a set of nanostructures tailored to precisely match a dark-field magneto-optical magnetometer have been fabricated and characterized. This work demonstrates the versatility of this hybrid technique and the interesting magnetic properties of the nanostructures produced, opening a promising route for the development of new 3D devices for applications and fundamental studies.