The comprehensive integration of instrumentation, communication, and control into physical systems has led to the study of Cyber-Physical Systems (CPSs), a field that has recently garnered increased attention. A key concern that is ubiquitous in CPS is a need to ensure security in the face of cyber attacks. In this paper, we carry out a survey of systems and control methods that have been proposed for the security of CPS. We classify these methods into three categories based on the type of defense proposed against the cyberattacks: prevention, resilience, and detection & isolation. A unified threat assessment metric is proposed in order to evaluate how CPS security is achieved in each of these three cases. Also surveyed are the risk assessment tools and the effect of network topology on CPS security. Furthermore, an emphasis has been placed on power and transportation applications in the overall survey.