Method of correcting systematic error in a metrology system

A computer program encoded in a computer readable medium containing program instructions for execution on a computer system, which when executed by the computer system, cause the computer system to perform the steps of:

• measuring a first diffraction spectrum from a standard substrate including a layer having a known refractive index and a known extinction coefficient by exposing the standard substrate to a spectrum of electromagnetic energy;
• calculating a tool-perfect diffraction spectrum for the standard substrate;
• calculating a hardware systematic error by comparing the measured diffraction spectrum to the calculated tool-perfect diffraction spectrum;
• measuring a second diffraction spectrum from a workpiece by exposing the workpiece to the spectrum of electromagnetic energy;
• and
• correcting the measured second diffraction spectrum based on the calculated hardware systematic error to obtain a corrected diffraction spectrum.