A method of preventing inter-system interference while acquiring waveforms in a test and measurement instrument with variation in a device under test system S-parameters. The method includes receiving a waveform from a device under test at the test and measurement instrument, digitizing the waveform, identifying portions of the digitized waveform with different S-parameter characteristics, separating the identified portions of the digitized waveform into different waveforms, and displaying the different waveforms to a user.