For decades computer architects pursued one primary goal: performance. Transistor scaling has translated into remarkable gains in operating frequency and reduction in power consumption. However, increased complexity from the device to architecture levels impose several new challenges, including a decrease in dependability/reliability due to physical failures. Reconfigurable platforms are highly susceptible to scaling related complexity, typically resulting in higher power consumption as compared to application-specific integrated circuits. The concern becomes far more important in the 3-D integrated circuit (IC) domain as vertically stacked blocks exhibit increased thermal resistance to the heat sink. The degradation in dependability becomes an important design challenge, not only for safety critical systems, but for the majority of architectures. In this paper, a framework used to explore alternative fault-tolerant schemes is proposed that masks the degradation in reliability for 3-D FPGA platforms. Simulation results at the RTL level highlight the benefits of the introduced solution, as the maximum operating frequency and power consumption are improved by 33% and 26%, respectively, as compared to similar state-of-the-art solutions.