Monolithic 3D (M3D) is a revolutionary technology for high-density and high-performance chip design in the post-Moore era. However, it suffers from considerable thermal confinement due to the transistor stacking and insulating materials between the layers. As a way of reducing power, thereby mitigating the thermal problem, we propose a comprehensive physical design methodology that incorporates two new important items, one is blockage aware MIV (monolithic inter-tier via) placement and the other is 3D net ordering for routing, intending to optimize wire length. Precisely, we propose a three-step approach: (1) retrieving the MIV region candidates for each 3D net, (2) fine-tuning placement to secure MIV spots in the presence of blockages, and (3) performing M3D routing with net ordering to consider the fine-tuned placement result. We implement the proposed M3D design flow by utilizing commercial 2D IC EDA tools while providing seamless optimization for cross-tier connections. In the meantime, our experiments confirm that proposed M3D design flow saves wire length per cross-tier net by up to 41.42%, which corresponds to 7.68% less total net switching power, equivalently 36.79% lower energy-delay-product over the conventional state-of-the-art M3D design flow.