Cyber-Physical Systems (CPS) are in most cases safety-and mission-critical. Standard design techniques used for securing embedded systems are not suitable for CPS due to the restricted computation and communication budget available in the latter. In addition, the sensitivity of sensed data and the presence of actuation components further increase the security requirements of CPS. To address these issues, it is necessary to provide new design methods in which security is considered from the beginning of the whole design flow and addressed in a holistic way. In this paper, we focus on the design of secure CPS as part of the complete CPS design process, and provide insights into new requirements on platform-aware design of control components, design methodologies and architectures posed by CPS design. We start by discussing methods for the multi-disciplinary modeling, simulation, tools, and software synthesis challenges for CPS. We also present a framework for design of secure control systems for CPS, while taking into account properties of the underlying computation and communication platforms. Finally, we describe the security challenges in the computing hardware that is used in CPS.