A system for characterizing periodic structures formed on a sample on a real time basis is disclosed. A spectroscopic measurement module generates output signals as a function of wavelength. The output signals are supplied to a processor for evaluation, which creates an initial theoretical model having a rectangular structure. The processor calculates the theoretical optical response of that sample, which is compared to normalized measured values at each of a plurality of wavelengths. The model configuration is then modified to be closer to the actual measured structure. The processor recalculates the optical response and compares the result to the normalized data. This process is repeated in an iterative manner until a best fit rectangular shape is obtained. Thereafter, the complexity of the model is iteratively increased, and model is iteratively fit to the data until a best fit model is obtained which is similar to the periodic structure.