A system and method determine an approximate structure of an object on a substrate. This may be applied in model based metrology of microscopic structures to assess critical dimension or overlay performance of a lithographic apparatus. A scatterometer is used to determine approximate structure of an object, such as a grating on a stack, on a substrate. The wafer substrate has an upper layer and an underlying layer. The substrate has a first scatterometry target region, including the grating on a stack object. The grating on a stack is made up of the upper and underlying layers. The upper layer is patterned with a periodic grating. The substrate further has a neighboring second scatterometry target region, where the upper layer is absent. The second region has just the unpatterned underlying layers.