A system for examining a patterned structure formed on a semiconductor wafer using an optical metrology model includes a first fabrication cluster, a metrology cluster, an optical metrology model optimizer, and a real time profile estimator. The first fabrication cluster processes a wafer, the wafer having a first patterned and a first unpatterned structure. The metrology cluster measures diffraction signals off the first patterned and first unpatterned structure. The metrology model optimizer optimizes an optical metrology model of the first patterned structure. The real time profile estimator creates an output comprising underlying film thickness, critical dimension, and profile of the first patterned structure.