A plasma reactor has a cylindrical microwave cavity overlying a workpiece processing chamber, a microwave source having a pair of microwave source outputs, and a pair of respective waveguides. The cavity has first and second input ports in a sidewall and space apart by an azimuthal angle. Each of the waveguides has a microwave input end coupled to a microwave source output and a microwave output end coupled to a respective one of the first and second input ports, a coupling aperture plate at the output end with a rectangular coupling aperture in the coupling aperture plate, and an iris plate between the coupling aperture plate and the microwave input end with a rectangular iris opening in the iris plate.