Disclosed are apparatus and methods for characterizing a plurality of structures of interest on a semiconductor wafer. A plurality of models having varying combinations of floating and fixed critical parameters and corresponding simulated spectra is generated. Each model is generated to determine one or more critical parameters for unknown structures based on spectra collected from such unknown structures. It is determined which one of the models best correlates with each critical parameter based on reference data that includes a plurality of known values for each of a plurality of critical parameters and corresponding known spectra. For spectra obtained from an unknown structure using a metrology tool, different ones of the models are selected and used to determine different ones of the critical parameters of the unknown structure based on determining which one of the models best correlates with each critical parameter based on the reference data.