A method and system are presented for optical measurements in multi-layer structures to determine the properties of at least some of the layers. The structure is patterned by removing layer materials within a measurement site of the structure from the top layer to the lowermost layer of interests. Optical measurements are sequentially applied to the layers, by illuminating a measurement area in the layer under measurements, when the layer material above said layer under measurements is removed, thereby obtaining measured data portions for the at least some of the layers, respectively. The properties of each of the at least some layers are calculated, by analyzing the measured data portion of the lowermost layer, and then sequentially interpreting the measured data portions of all the other layers towards the uppermost layer, while utilizing for each layer the calculation results of the one or more underlying layers.