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In this paper, an embedded electromagnetic bandgap structure is proposed for harmonic filtering of differential signal's undesired common mode components. Rather than use lumped circuit components and likely causing some degradation to the intended high speed differential signal, the embedded planar common mode filter causes no degradation to the intended signal, and enhances the signal integrity and electromagnetic compatibility performance of the system. Single ended and differential traces are considered and the impact of the common mode filtering is measured in terms of mixed mode scattering parameters and eye diagram metrics. The systematic procedure to design such a structure is outlined, and its design robustness is also verified.