Ferromagnetic materials have been utilized as recording media in data storage devices for many decades. The confinement of a material to a two-dimensional plane is a significant bottleneck in achieving ultra-high recording densities, and this has led to the proposition of three-dimensional (3D) racetrack memories that utilize domain wall propagation along the nanowires. However, the fabrication of 3D magnetic nanostructures of complex geometries is highly challenging and is not easily achieved with standard lithography techniques. Here, we demonstrate a new approach to construct 3D magnetic nanostructures of complex geometries using a combination of two-photon lithography and electrochemical deposition. The magnetic properties are found to be intimately related to the 3D geometry of the structure, and magnetic imaging experiments provide evidence of domain wall pinning at the 3D nanostructured junction.