The extension of nanoscale quantum materials to the third dimension brings new possibilities to geometrically tune emergent properties, emulating or indeed going beyond the physics of bulk materials, with exciting implications for high-density technological integration. Realising such three-dimensional architectures requires nanofabrication techniques that not only enable complex 3D geometries, but also deliver functional quantum materials with emergent phenomena. Recent advances in focused electron- and ion-beam induced deposition (FEBID and FIBID) have made 3D nanopatterning of functional materials in complex geometries increasingly feasible, paving the way for the experimental realisation of new phenomena and device prototyping. In this review, we discuss the use of FEBID and FIBID 3D nanopatterning of superconducting and magnetic materials. We address the underlying mechanisms, and capabilities of these techniques, focusing on the physical phenomena that become accessible. Considering the resolution of the techniques in the context of the fundamental lengthscales of the materials, we discuss the emergent effects that arise due to three dimensional geometries in magnetic and superconducting nanostructures, and highlight perspectives for future developments of the techniques.