The problems involved in securing cyber-physical systems are well known to the critical infrastructure protection community. However, the diversity of cyber-physical systems means that the methods used to analyze system security must often be reinvented. The issues of securing the physical assets of a system, the electronics that control the system and the interfaces between the cyber and physical components of the system require a number of security tools. Of particular interest is preventing an attacker from exploiting nondeducibility-secure information flows to hide an attack or the source of an attack. This potentially enables the attacker to interrupt system availability.This chapter presents an algorithm that formalizes the steps taken to design and test the security of a cyber-physical system. The algorithm leverages information flow security techniques to secure physical assets, cyber assets and the boundaries between security domains.