A cyber-physical system (CPS) is a composition of independently interacting components, including computational elements, communications and control systems. Applications of CPS institute at different levels of integration, ranging from nation-wide power grids, to medium scale, such as the smart home, and small scale, e.g. ubiquitous health care systems including implantable medical devices. Cyber-physical systems primarily transmute how we interact with the physical world, with each system requiring different levels of security based on the sensitivity of the control system and the information it carries. Considering the remarkable progress in CPS technologies during recent years, advancement in security and trust measures is much needed to counter the security violations and privacy leakage of integration elements. This paper focuses on security and privacy concerns at different levels of the composition and presents system level solutions for ensuring the security and trust of modern cyber-physical systems.