In electromagnetic compatibility (EMC) design, it is important to mitigate the dominant effect among those caused by many unintentional parasitic elements or couplings. However, the dominant effect is usually unclear and hence EMC engineers often resort to trial and error to find an effective counterplan. This paper presents an approach for aiding engineers in finding a better design plan using topology optimization, which is a simulation-based structural optimization method. The proposed approach is applied to the conductor pattern design in simple circuits of electromagnetic interference filters, in which the dominant effect is conduction or induction noise depending on the circuit parameters. It is demonstrated that a structure with a reduced dominant effect is obtained automatically, and the utilization of the optimized result for EMC design is also discussed.