A method and system are provided for controlling processing of a structure. First measured data is provided being indicative of at least one of: a thickness (d2) of at least one layer (L2) of the structure W in at least selected sites of the structure prior to 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: a thickness of the processed 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 determine a thickness (d′1 or d′2) of at least one layer of the processed structure. This determined thickness is indicative of the quality of processing.