The function of the living matter from biomolecules to the whole body of the organism is based on the structure. Consequently, structural information is essential for the understanding of the function of living organisms. The biological structures from biomolecules to cells and tissues are intimately related to each other, and changing their morphological, biochemical, and physiological properties dynamically according to the developmental and functional status of the organism. The molecular dynamics of living matter should be related to the function of whole body. We employed HVEM stereoscopy and morphometry for the purpose of combining the structural information at nanometer level with those of the micrometer level. Novel aspects of three-dimensional organization of neuronal and glial cell processes have been presented. This structural information together with morphometrical data could contribute to the elucidation of brain function.