An Overview of Three-Dimensional Integration and FPGAs -- Three-Dimensional Integration: A More Than Moore Technology -- Field Programmable Gate Arrays: An Overview -- Two Dimensional FPGAs: Configuration and CAD Flow -- Three-Dimensional FPGAs: Configuration and CAD Development -- Three-Dimensional Tree-based FPGA: Architecture Exploration Tools and Technologies -- Three-Dimensional Thermal Modeling: Tools and Methodologies -- Physical Design and Implementation of 3D Tree-based FPGAs -- Three-Dimensional FPGAs: Future Lines of Research.