1. A method comprising: processing a sample having at least a first layer and a second layer that is under the first layer to at least partially remove the first layer to produce a post-processed sample; performing a post-processing measurement of the post-processed sample; generating a first model of the post-processing sample, wherein the first model models the first layer as an independent variable and models the second layer; generating a second model of the post-processing sample, wherein the second model models the first layer as having a thickness of zero and models the second layer as an independent variable; using the post processing measurement, the first model and the second model to determine at least one desired parameter of the post-processed sample.