A method is described for processing an electrical stimulation response measurement waveform signal measured in response to delivery of a selected electrical stimulation signal to neural tissue. The electrical stimulation response measurement waveform signal contains a stimulus artifact and one or more neuronal action potentials. The electrical stimulation signal is selected based on satisfying a cost function comparison between at least one stimulus artifact component and a plurality of known neuronal action potential waveforms. The electrical stimulation response waveform signal is then processed using a source separation algorithm to remove the stimulus artifact component.
