Abstract: A method of compensating for a contribution of conductivity of the semiconductor wafer to a measured trace by an in-situ electromagnetic induction monitoring system includes storing or generating a modified reference trace. The modified reference trace represents measurements of a bare doped reference semiconductor wafer by an in-situ electromagnetic induction monitoring system as modified by a neutral network. The substrate is monitored with an in-situ electromagnetic induction monitoring system to generate a measured trace that depends on a thickness of the conductive layer, and at least a portion of the measured trace is applied to a neural network to generate a modified measured trace. An adjusted trace is generated, including subtracting the modified reference trace from the modified measured trace.