Three dimensional macro structures consisting of nanostructures with well-defined dimensions and properties is attracting significant interest for fields including electronics, photonics, nanofluidics, medicine, sensing, catalysis, controlled release, and others. To date, fabrication of 3D macrostructures in large scale has posed an outstanding challenge. Atomic layer deposition (ALD) is stepwise, surface self-limited vacuum-based thin film deposition technique, and is able to produce thin films and overlayers of different materials (inorganic, organic, hybrid) on highly complex structures with sub-nm thickness uniformity and conformality control. In our work, Al₂O₃ and ZnO ALD were successfully applied onto 3D poly vinyl alcohol electrospun fiber matrix templates to fabricate Al₂O₃, ZnO and coaxial Al₂O₃/ZnO nanotubes with precisely controlled tube wall thickness. Moreover, we show when coaxial Al₂O₃/ZnO nanotubes are annealed at high temperature, the Kirkendall effect results in formation of unique nanocomposite materials, including interpenetrating nanotubes, as shown by Figure 1a-c. Furthermore, we show that subsequent surface functionalization of the Al₂O₃ nanotube matrix, for example using 3-aminopropyltriethoxy silane, enable further reactions and assembly of complex structures as shown in Figure 1d. This method represents a robust and inexpensive way to synthesize 3D nanomaterials in large scale.