Ion isolation was achieved via selective pulsing of the entrance and exit ion mirrors in an electrostatic linear ion trap mass spectrometer (ELIT). Mirror switching has been described previously as a method for capturing injected ions in ELIT devices. After ion trapping, mirror switching can be used as a method for ion isolation of successively narrower ranges of mass-to-charge (m/z) ratio. By taking advantage of the spatial separation of ions in an ELIT device, pulsing of the entrance and/or exit mirrors can release unwanted ions while continuing to store ions of interest. Furthermore, mirror switching can be repeated multiple times to isolate ions of very similar m/z values with minimal loss of the stored ions, as is demonstrated by the isolation of protonated l-glutamine and l-lysine (Δ m/z = 0.0364) from a mixture of the two amino acid ions and the isobaric mixture of [PC P-18:0/22:6] and [PC 19:0/19:0] (Δ m/z = 0.0575). As isolation is accomplished due to the spatial/temporal separation of ion packets within the ELIT, multiple reflection-time-of-flight (MR-TOF) mass spectra are shown to demonstrate separation in the ELIT at the time of isolation. An isolation resolution of greater than 35 000 fwhm is demonstrated here using a 5.25 in. ELIT. This resolution corresponds to the fwhm resolution necessary to reduce contaminant overlap of an equally abundant adjacent ion to 1% or less of the isolated ion intensity.