It is known that conventional scaffold manufacturing techniques have low reproducibility and control of the micro-architecture features. Although there have been advances in bone tissue engineering fabrication, there is no consensus on the optimized parameter designs or clear understanding of the microfluidic interactions required for tissue regeneration. In this work, we introduce a new inexpensive fabrication method of producing pore designs of 3D-elastomeric structures with high controlled geometry of orthogonal arrays. The present fabrication method utilizes a permanent and reusable micro-machined mould along with a micro-casted process to efficiently fabricate diverse 3D feature directly. This fabrication method, without multiple process steps, would be suitable to support experiments of controlled environment for flow effects in 3D bone scaffolds.