Methods and systems for reducing wafer shape and thickness measurement errors resulted from cavity shape changes are disclosed. Cavity calibration process is performed immediately before the wafer measurement. Calibrating the cavity characteristics every time the method is executed reduces wafer shape and thickness measurement errors resulted from cavity shape changes. Additionally or alternatively, a polynomial fitting process utilizing a polynomial of at least a second order is utilized for cavity tilt estimation. High order cavity shape information generated using high order polynomials takes into consideration cavity shape changes due to temperature variations, stress or the like, effectively increases accuracy of the wafer shape and thickness information computed.