Three-phase multi-stage filters are widely adopted in modern power electronics due to their superior attenuation characteristics. However, the self and mutual parasitic couplings of the filter sub-components are known to degrade the filter performance significantly. Most importantly, near field effects are prominent when dealing with high density packaging of multi-stage filters. Therefore, it is essential to decouple these effects. In this regard, this paper proposes novel component placement, winding strategy as well as shielding and grounding techniques to desensitize the influence of the parasitic effects on a three-phase multi-stage filter. These methodologies could serve as a design guideline for EMI filters having different inductor and capacitor form-factors.