1. A system for creating a mathematical model according to a multivariate analysis, the system comprising: a. means for acquiring metrology data for semiconductor wafers at the conclusion of a final process step for a manufacturing process; b. means for acquiring data for a plurality of process variables for a first process step for manufacturing semiconductor wafers; c. a model generation module for creating a first mathematical model of the first process step based on the metrology data and the acquired data for the plurality of process variables for the first process step; d. means for acquiring data for a plurality of process variables for at least a second process step for manufacturing the semiconductor wafers and a model generation module for creating a second mathematical model of the first process step based on the metrology data and the acquired data for the plurality of process variables for the first process step; e. a model generation module for creating an n th mathematical model based on the metrology data and the data for the plurality of process variables for each of the n process steps; and f. a model generation module for creating a top level mathematical model based on the metrology data and the models created by elements c., d. and e., the top level mathematical model being based on those process variables that have a substantial effect on the metrology data.