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A modeling scheme is proposed and tested for the analysis of waveguide-based quasi-optical systems. The system is partitioned into blocks, each block is characterized by its generalized scattering matrix (GSM) which in turn are cascaded to obtain the model of the complete system. Blocks with active devices are accounted for in the GSM by means of circuit ports. The calculated and measured results for a Ka-band double layer patch array is presented. A good agreement between theory and measurement is obtained.