Recent advancements in additive manufacturing enable the preparation of free-shaped 3D objects with feature sizes down to and below the micrometer scale. While 3D nanoprinting enables the fabrication of nanostructures with significant morphological complexity, adding material functionalities to the current fabrication scheme is one of the main priorities for the further development of this technology. In this respect, hybrid approaches can be considered for a site-selective modication and functionalization of morphologically complex geometries. The combination of the free-shaped 3D nano-writing with established chemical vapor deposition (CVD) techniques provides unique opportunities to synthesize complex 3D core-shell heterostructures. Hence, this hybrid approach enables the fabrication of morphologically tunable layer-based nanostructures with great potential of unlocking new functionalities. Here, the fundamentals of such a hybrid approach are demonstrated by preparing core-shell heterostructures using 3D scaffolds printed by focused electron beam induced depositoin (FEBID) for site-selective CVD. In particular, 3D micro-bridges are printed by FEBID with the (CH₃)₃CH₃C₅H₄Pt precursor and coated by thermal CVD using the Nb(NMe₂)₃(N-t-Bu) and HFeCo₃(CO)₁₂ precursors. Two model systems based on CVD layers consisting of a superconducting NbC-based layer and a ferromagnetic Co₃Fe layer are prepared and characterized with regard to their composition, microstructure and magneto-transport properties. Finally, localized temperature management within the scaffold resistor can be achieved by tuning the conductivity, e.g., by modulating the 3D structure. Hence, specic areas become accessible allowing for local CVD deposition without affecting the surrounding chip design.