There are several "disconnects " which need to be addressed to provide effective means for engineering Cyber Physical Systems (CPS). One of them is how to construct an optimized application starting from high-level specifications taking into account exacerbated interactions with the physical environment and in the same time addressing new paradigms like mixed criticality, and distributed multi/many-cores platforms. We introduce in this position paper a new methodology called model-compilation for Cyber-Physical systems. This methodology introduces new concepts and process that can be seen as a specification that tool editors and CPS application developers can integrate (instantiate) in their tool chain or development process.