Three-dimensional (3D) field-programmable gate arrays (FPGAs) are expected to offer higher logic density as well as improved delay and power performance by utilizing 3D integrated circuit technology. However, because through-silicon-vias (TSVs) for conventional 3D FPGA interlayer connections have a large area overhead, there is an inherent tradeoff between connectivity and small size. To find a balance between cost and performance, and to explore 3D FPGAs with realistic 3D integration processes, we propose two types of 3D FPGA and construct design tool sets for architecture exploration. In previous research, we created a TSV-free 3D FPGA with a face-down integration method; however, this was limited to two layers. In this paper, we discuss the face-up stacking of several face-down stacked FPGAs. To minimize the number of TSVs, we placed TSVs peripheral to the FPGAs for 3D-FPGA with 4 layers. According to our results, a 2-layer 3D FPGA has reasonable performance when limiting the design to two layers, but a 4-layer 3D FPGA is a better choice when area is emphasized.