In this chapter, we adopt a holistic cross-layer viewpoint towards a hierarchical structure of ICS and the attack models. The physical layer is comprised of devices, controllers and the plant whereas the cyber layer consists of routers, protocols, and security agents and manager. The physical layer controllers are often designed to be robust, adaptive, and reliable for physical disturbances or faults. With the possibility of malicious behavior from the network, it is also essential for us to design physical layer defense that take into account the disturbances and delay resulting from routing and network traffic as well as the unexpected failure of network devices due to cyber-attacks. On the other hand, the cyber security policies are often designed without consideration of control performances. To ensure the continuous operability of the control system, it is equally important for us to design security policies that provide maximum level of security enhancement but minimum level of system overhead on the networked system. The physical and cyber aspects of control systems should be viewed holistically for analysis and design.