A substrate etching system includes an etching control module, a filtering module, and an endpoint module. The etching control module selectively begins plasma etching of a substrate within an etching chamber. The filtering module, during the plasma etching of the substrate: receives a signal including endpoint information; decomposes the signal using empirical mode decomposition (EMD); and generates a filtered signal based on results of the EMD. The endpoint module indicates when an endpoint of the plasma etching of the substrate has been reached based on the filtered signal. The etching control module ends the plasma etching of the substrate in response to the indication that the endpoint of the plasma etching of the substrate has been reached.