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A 3D edge finite element analysis is presented to calculate the resonance frequencies and quality factors of inhomogeneously loaded cavity resonators (filters) terminated by waveguides (ports). The matching of the ports is modeled by perfectly matched layers (PML). The selection of the PML parameters is discussed. A complex nonlinear eigenvalue problem is obtained which is solved by a special solver with the sparsity of the matrices fully utilized. An approximation is applied to reconstruct the frequency response of the scattering parameters from the field calculated at the resonance frequencies.