Native composite materials such as wood, exhibit complex fiber arrangements to enhance strength, flexibility, and functionality. This work presents a new method enabling three-dimensional (3D) characterization of crystalline fibril organization at the nanoscale using Scanning Electron Diffraction (SED), enabling analysis of beam-sensitive materials.SED utilizes a nanoscale electron beam, rapidly scanning the specimen while synchronously capturing diffraction patterns. While SED effectively provides quantitative mapping of the local crystalline organization[1], it is by nature providing 2D information. Herein, we introduce a method based on multiple 2D projections and an iterative algorithm for reconstructing three-dimensional fibril structures.Using this method, we have successfully mapped the hierarchical organization of cellulose nanofibrils in the cell walls of native birch and oat husk, including their helical fibril arrangements. In birch, we observe a two-layer structure with opposite helical orientations and the smooth transition in between. The outer S1 layer forms a left-handed helix, while the inner S2 layer assumes a right-handed configuration with a larger pitch. In contrast, oat husk exhibits a multilayered cell wall with alternating fibril handedness across layers (see Figure 1).This advancement in 3D characterization provides unique nanoscale insights into the hierarchical organization of fibrous biomaterials, paving the way for the next generation of bio-inspired materials with customized mechanical properties.