Organized networks are common in nature showing specific tissue micro-architecture, where cells can be found isotropically or anisotropically distributed in characteristic arrangements and tissue stiffness. However, when addressing an in vitro tissue model, it is challenging to grant control over mechanical properties while achieving anisotropic porosity of polymeric networks, especially in three-dimensional systems (3-D). While progress was achieved organizing cells in two-dimension (2-D), fabrication methods for aligned networks in 3-D are limited. Here, we describe the use of a biomimetic extra-cellular matrix system allowing programming of anisotropic structures into precisely advancing pore diameters in 3-D. Using control over polymeric composition, crosslinking directionality and freezing gradient dynamics, we revealed a mechanism to top-down biofabricate 3-D structures with tunable micro-porosity capable of directing cellular responses at millimeter scale such as axonal anisotropic outgrowth that is a unique characteristic of the brain cortex. Further, we showed the unique integration of this method with a microfluidic system establishing a neural-endothelial heterotypic conjugation, which can potentially be broadly applied to multiple organ systems.