Modern FPGAs have become a viable alternative to cell-based design technology by providing re-configurable computing platforms with improved performance and higher density using 3D integration technology. While the re-configurability provides flexibility, FPGAs also lead to area and performance overhead in comparison to cell-based custom integrated circuits (ICs). Thus to combine the advantages of both FPGAs and custom ICs, modern 3D heterogeneous FPGAs emerged as an attractive solution for system-on-chip implementations. The modern FPGAs include design components such as digital signal processors, on chip memory blocks, multipliers, adders, and entire processors. In this chapter our primary focus is on teaching the development of 3D FPGA tools and technologies and the validation of architecture exploration tools and optimization methodologies by using custom designed 3D homogeneous and heterogeneous Tree-based FPGAs.