Methods and systems for estimating values of parameters of interest of structures fabricated on a wafer with a signal response metrology (SRM) model trained based on reference measurement data collected from the same wafer are presented herein. In one aspect, the SRM model is an input-output model trained to establish a functional relationship between reference measurements of structures fabricated on the wafer to raw measurement data collected from the same wafer. The raw measurement data collected from the wafer is employed for training the SRM model and for performing measurements using the trained SRM model. In another aspect, the SRM model uses the entire set of raw measurement data collected from a number of measurement sites across the wafer for both training and subsequent measurement at each individual site. In a further aspect, the SRM model is trained and utilized to measure each parameter of interest individually.