A system, method and computer program product are provided for calibrating metrology tools. One or more design-of-experiments wafers is received for calibrating a metrology tool. A set of signals is collected by measuring the one or more wafers utilizing the metrology tool. A first transformation is determined to convert the set of signals to components, and a second transformation is determined to convert a set of reference signals to reference components. The set of reference signals is collected by measuring the one or more wafers utilizing a well-calibrated reference tool. A model is trained based on the reference components that maps the components to converted components, and the model, first transformation, and second transformation are stored in a memory associated with the metrology tool.