Physically unclonable functions (PUFs) provide a basis for many security, and digital rights management protocols. PUFs exploit the unclonable and unique manufacturing variability of silicon devices to establish a secret. However, as we will demonstrate in this work, the classic delay-based PUF structures have a number of drawbacks including susceptibility to prediction, reverse engineering, man-in-the-middle and emulation attacks, as well as sensitivity to operational and environmental variations. To address these limitations, we have developed a new set of techniques for design and implementation of PUF. We design a secure PUF architecture and show how to predict response errors as well as to compress the challenge/responses in database. We further demonstrate applications where PUFs on reconfigurable FPGA platforms can be exploited for privacy protection. The effectiveness of the proposed techniques is validated using extensive implementations, simulations, and statistical analysis.