Cyber Physical Systems (CPS) are networked systems of cyber (computation and communication) and physical (sensors and actuators) components that interact in a feedback loop with the possible help of human intervention, interaction and utilization. These systems will empower our critical infrastructure and have the potential to significantly impact our daily lives as they form the basis for emerging and future smart services. On the other hand, the increased use of CPS brings more threats that could have major consequences for users. Security problems in this area have become a global issue, thus, designing robust, secure and efficient CPS is an active area of research. Security issues are not new, but advances in technology make it necessary to develop new approaches to protect data against undesired consequences. New threats will continue to be exploited and cyber-attacks will continue to emerge, hence the need for new methods to protect CPS. This paper presents an analysis of the security issues at the various layers of CPS architecture, risk assessment and techniques for securing CPS. Finally, challenges, areas for future research and possible solutions are presented and discussed.