A filter optimization strategy based on full wave EM simulations is proposed. With the introduction of additional internal ports in the filter model, the Multi-Port Admittance-Matrix (Y-Matrix) is obtained. The main advantage lies in the fact that the filter’s basic parameters, as there are the resonant frequency of each resonator, the coupling coefficients and the external Qs are directly accessible through the Multi-Port Y-Matrix. These values are known to give a broad insight into the filter and allow a straightforward optimization procedure to meet the specified data of the synthesis. Furthermore, parasitic effects and design restrictions can be identified and even quantified. Here, an example of a combline filter with a six pole Chebyshev characteristic has been chosen to demonstrate the technique and to verify the method, which can be adapted to other types of filters as well as to other characteristics. Based on this example, a parasitic external coupling was identified and compensated illustrating the advantages of this method.