Wood is a hierarchical composite, consisting at its lowest hierarchy level of crystalline cellulose elementary fibrils with diameters of 2–4 nm embedded in a matrix of hemicelluloses and lignin. At the micrometer scale, it has a cellular architecture resembling a honeycomb structure. The transformation of the hierarchical wood structure into a silica replica has been reported recently. Its formation process and structural details are studied in this contribution. First, a silica/biopolymer composite is prepared by wood delignification and cell-wall modification, followed by silica precursor infiltration and condensation. The calcination process is monitored to gain insight into the structure development upon decomposition of the biopolymers. The material changes its architecture gradually from fibrillar structures of 10–20 nm in diameter with homogeneous electron density, into fibrils of 8–10 nm in diameter with inhomogeneous electron density, exhibiting internal sub-fibrillar structures of about 2 nm in diameter. The steps of the successful replication of the cellulose elementary fibrils into nanopores of similar diameter and orientation in a fibrillar silica matrix are demonstrated. These nanopore replicas of the original cellulose are wound in a steep helix within the macropore walls. These advanced materials may have lightweight structural applications and the nanopores may be advantageous for molecular separation.