Provided is a method of controlling a photolithography cluster or a subsequent fabrication cluster using optical metrology to determine profile parameters of a photomask structure covered with a pellicle. An optical metrology model of the pellicle is developed and integrated with the optical metrology model of the photomask structure. The optical metrology model of the photomask taking into account the optical effects on the illumination and detection beams transmitted through the pellicle and diffracted by the photomask structure. One or more profile parameters of the photomask structure is determined and used to adjust one or more process parameters or equipment settings of a photolithography cluster using the photomask or a subsequent fabrication cluster.