The improved glenoid fossa prosthesis for repair of a scapular deficient patient includes a base with a fixed flange, and a separable flange. A conical taper on the base and a complimentary locator edge positively orient the separable flange when joined with the base for affixation by screw. A plurality of flange fixation screws penetrates the scapular tissue between the flanges for affixation of the flanges thereto. The flange thickness is variable to approximate the topography of the scapular tissue in the affixation area to minimize tissue trimming during fitment. A cutting mask attaches to the deficient scapula in the glenoid fossa area to guide the physician in trimming scapular tissue for fitment. A cortical screw further fixates the base to the scapular tissue. A second conical taper on the base serves as a mount for a glenoid sphere (reverse shoulder) or socket (standard shoulder) repair configuration.