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A hybrid mode-matching(MM)/finite element (FE) CAD method is applied for the fast CAD of ultra-wide stop band and high return loss waffle-iron filters. The design is based on cascaded waffe-iron sections with a different number of bosses in the cross-sections utilizing a new non-isotropic waffle-iron structure with individually optimized lengths. For the efficient optimization with regard to the S parameters, the generalized scattering matrix (GSM) combination technique is used with an automatic selection of localized and accessible modes. An overall block-LU-decomposition method allows one to calculate the field intensities within the waffle-iron sections. The optimization carried out by a robust direct search method achieved a waffle-iron filter with better than 30dB return loss between 7 and 8.3 GHz, and more than 70 dB rejection between 12 and 60 GHz. The theory is verified by excellent agreement with measurements.