With the advent of wide bandgap (WBG) semiconductor devices, the electromagnetic interference (EMI) emissions are more pronounced due to high slew rates in the form of high dv/dt and high di/dt at higher switching frequencies compared to the traditional silicon technology. To comply with the stringent conducted emission requirements, EMI filters are adopted to attenuate the high frequency common mode (CM) and differential mode (DM) noise through the propagation path. However, self and mutual parasitic components are known to degrade the EMI filter performance. While parasitic cancellation techniques have been discussed at length in prior literature, most of them have focused mainly on single phase applications. As such this work focuses on extending the preexisting concepts to three-phase systems. Novel component placement, winding strategy as well as shielding and grounding techniques were developed to desensitize the influence of the parasitic effects on a three-phase multi-stage filter. The effectiveness of the three-phase filter structure employing the proposed methodologies has been validated via noise measurements at the line impedance stabilization network (LISN) in a 15kW rated motor drive system. Consequently, general design guidelines have been formulated for filter topologies with different inductor and capacitor form-factors.