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A central challenge in designing embedded control systems or cyber-physical systems (CPS) is that of translating high-level models of control algorithms into efficient implementations, while ensuring that model-level semantics are preserved. While a large body of techniques for designing provably correct control strategies exist in the control theory literature, when it comes to transforming mathematical descriptions of these strategies to an efficient implementation, the available means are surprisingly ad hoc in nature. Among other reasons, this is because of (i) implementation platform details not sufficiently being accounted for in controller models, (ii) side effects introduced in the code generation process, (iii) various compiler optimizations whose impact on the dynamics of the plant being controlled not being properly understood, (iv) the presence of analog components on the implementation platform whose behavior is difficult to model, (v) computation and communication delays that exist in an implementation but were not accounted for in the model, and (vi) also the effects of image/video processing whose accuracy and timing behavior are difficult to model. As we move towards designing autonomous systems, these issues become biting problems on the path to certification, and striking a balance between performance and certification. In this position paper, we discuss some of these challenges - that we formulate as the need for modeling the interactions between various implementation layers in a CPS - and potential research directions to address them.