The objective of the proposed research is to develop the first open and reproducible RTL-to-GDSII design flow for both 2D and 3D FPGA fabrics. The research bridges the gap between high-level architectural exploration and manufacturable physical implementation by extending the open-source OpenROAD framework to support FPGA-specific and 3D-aware design features. The proposed flow will take architectural and RTL outputs generated by LaZagna as inputs and produce sign-off-quality layouts and analysis reports, including timing, power, IR-drop, and thermal metrics. Key research scope includes architecture-guided floorplanning, tier-aware placement and routing, bonding-technology modeling, and integrated power and thermal co-simulation. In addition, the research will incorporate ML and AI to enable early prediction and intelligent optimization within the physical design loop. Together, these contributions aim to establish an open, intelligent, and physically validated design framework that significantly accelerates design turnaround time, improves physical design quality, and provides a scalable foundation for future 3D FPGA and architecture-fabric co-design research.