Cellular processes in brain tissue such as migration, proliferation, morphology, and differentiation are influenced by mechanical cues, demonstrating the interplay between the structure and function. Given the complexity, it remains a substantial challenge to establish a reliable in vitro model mimicking structural properties as brain tissue. To address this challenge, we propose an innovative approach to create vertical hydrogel stacks based on microfluidic technology. 3D-printed microfluidic features in the sidewall profile of our chip designs allowed us to faithfully replicate these capillary force flow pinning structures in polydimethylsiloxane. After the successful application of hydrogel of a defined height, thanks to the pinning process and plating of stem-cell-derived neurons, the results demonstrated the potential of our BoC platform, providing a valuable tool for neuroscience research.