A waveguide flange system connects a pair of microwave components each having a flange attached thereto. Each flange includes a waveguide central bore, a knife edge surrounding the central bore on one side of the flange, and a weld plate extending orthogonal to the central bore in all directions. A deformable gasket is placed between the two flanges and engages the knife edges. A waveguide clamp assembly applies a uniform compressive force to clamp the flanges together to deform the gasket and to form the RF seals. The weld flanges are tack welded, the clamp removed, and the weld completed to form the vacuum seal. A venting trough through the knife edges provides a path for gasses from the region between the weld and the knife edge to vent to the central bore. The clamp may optionally be replaced after the welding for added strength and protection.