Recent advances in the size and performance of FPGAs, coupled with advantages in time-to-market, field-reconfigurability and lower up-front costs, make FPGAs ideally suited to a wide range of commercial and defense applications [6]. In addition, FPGAs’ generality and reconfigurability provide important protections against the introduction of Trojan horses during semiconductor manufacturing process[8]. As a result, FPGA applications increasingly involve highly-sensitive intellectual property and trade-secrets, as well as cryptographic keys and algorithms.