A method and system are presented for use in controlling the processing of a structure. First measured data is provided being indicative of at least one of the following: a thickness (d2) of at least one layer (L2) of the structure W in at least selected sites of the structure prior to the processing of the structure, and a surface profile of the structure prior to processing. An optical measurement is applied to at least the selected sites of the structure after processing and second measured data is generated being indicative of at least one of the following: a thickness of the process structure (d′) and a surface profile of the processed structure. The second measured data is analyzed by interpreting it using the first measured data to thereby determine a thickness (d′1 or d′2) of at least one layer of the process structure. This determined thickness is thus indicative of the quality of the processing.