We have developed an in situ focused ion beam measurement technique, which has applications for the accurate, controlled, and reproducible removal of material for high aspect ratio nanometer scale cuts in tracks. This technique uses the resistance change of a track, as it is milled by ions, to monitor in real time the thickness and the end point. We have compared this technique with the thickness measurements by atomic force microscope for 1 mu m wide cuts. The technique has an accuracy of a few nanometers.