A system is provided for processing wafers, such as silicon and silicon-on-insulator wafers. The processing includes thinning and flattening of the wafers at a work station located directly beneath a down looking metrology apparatus for directing light onto the wafer and measuring the light wavefronts reflected from the wafer. The metrology apparatus for flattening includes the feature of a multiple lens array for arranging the reflected wavefronts into a plurality of light spots, and a charge-coupled-device light responsive device for receiving the light spots and determining the shape of the wavefronts. The system also provides a wafer transport system for moving one or more wafers into one or more work stations beneath the metrology apparatus in a vacuum chamber.