Today, two-dimensional nanoscale magnetic systems are well understood, being used in applications from spintronic circuits to automotive sensing. Despite the great progress achieved in the field during the last decades, the development of three-dimensional devices is still hindered by phenomenal patterning and characterization challenges. Most lithographic and probing techniques have historically targeted planar samples and are not suitable for three dimensional geometries. This thesis achieves three key points to overcome these fabrication and characterization challenges: improving the understanding and control of 3D nano-printing of cobalt nanostructures using Focused Electron Beam Induced Deposition (FEBID), improving the performance of synchrotron-based magnetic X-ray microscopy in 3D geometries and adapting existing magneto-optical techniques to rapidly probe 3D nanostructures in the lab. As a result of this work, new tools and skills are available in the field of 3D nano-magnetism, unlocking a path for the development of sophisticated 3D nanomagnetic devices with increased functionality and performance.