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We propose a computer-aided design tool of complex passive microwave devices in rectangular waveguide technology by hybridizing the finite element method and a modified multimodal variational formulation. The finite element method characterizes waves in the arbitrarily shaped discontinuities and the total response of the circuit is obtained by applying the modified multimodal variational formulation. The size of the scattering matrix of the total circuit depends only on the number of accessible modes in the beginning and the end of the overall structure. This feature makes the computation time of our hybrid method independent from distances between discontinuities of the circuit. The proposed hybrid method is successfully applied to the full-wave analysis of filters with great practical interest (i.e., multimode filters), thus improving computation time and memory storage against several full-wave finite element method based computer aided design tools.