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Modern embedded systems rely on cryptographic co-processors to ensure security. These cryptographic coprocessors are theoretically secure but their physical implementations are vulnerable against Side-Channel Attacks (SCA). This paper puts forward a methodology to evaluate the robustness of embedded systems against such attacks and therefore enhance user trust. We propose an evaluation framework composed of five distinct phases which are characterization, simulation, acquisition, pre-processing and analysis. The paper will also highlight common pitfalls made by evaluators and their solutions.