Hydroxyapatite (HA) bone scaffolds characterized by highly organized hierarchical structures have been obtained by chemically transforming native woods through a sequence of thermal and hydrothermal processes. The whole chemical conversion has been carried out through five steps from native wood to porous hydroxyapatite: 1) pyrolysis of ligneous raw materials to produce carbon templates characterized by the natural complex anisotropic pore structure; 2) carburization process by vapour or liquid calcium permeation to yield calcium carbide; 3) oxidation process to transform calcium carbide into calcium oxide; 4) carbonation by hydrothermal process under CO2 pressure for the further conversion into calcium carbonate; 5) phosphatization process through hydrothermal treatment to achieve the final hydroxyapatite phase. The five steps of the phase transformation process have been set up in order to achieve total phase conversion and purity maintaining the original native microstructure. An innovative biomimetic apatite hierarchically structured in parallel fastened hollow microtubules has been synthesized, structurally characterized and proposed as a new inorganic biomorphic scaffold providing a biomimetic nanostructure surface for fascinating bone engineering applications.