A metrology system includes a controller coupled to a detector to generate a detection signal based on the reflection of an illumination beam from a multilayer film stack. The multilayer film stack may include one or more zones with a repeating pattern of two or more materials. The controller may generate a model of reflection of the illumination beam by modeling the zones as thick films having zone thicknesses and effective permittivity values using an effective medium model relating the effective permittivity values of the zones to permittivity values and volume fractions of constituent materials. The controller may further determine values of the zone thicknesses and the volume fractions using a regression of the detection signal based on the effective medium model and further determine average thickness values of the constituent materials based on the number of films, the zone thicknesses, the volume fractions, and the effective permittivity values.