The disclosure provides a method for preparing a cross-section of a sample by milling with a focused ion beam. The cross-section is to be prepared at a pre-defined position. The method includes excavating a trench by milling in a first milling direction. The first milling direction leads away from the position of the cross-section to be prepared. The method also includes excavating the cross-section by enlarging the trench by milling in the reversed milling direction. The second milling direction leads towards the position of the cross-section to be prepared, whereupon the milling is completed at the position where the cross-section is to be cut. The desired largest milling depth is achieved at the completion of this milling step.

Methods for processing of a workpiece are disclosed. The actual rate at which different portions of an ion beam can process a workpiece, referred to as the processing rate profile, is determined by measuring the amount of material removed from, or added to, a workpiece by the ion beam as a function of ion beam position. An initial thickness profile of a workpiece to be processed is determined. Based on the initial thickness profile, a target thickness profile, and the processing rate profile of the ion beam, a first set of processing parameters are determined. The workpiece is then processed using this first set of processing parameters. In some embodiments, an updated thickness profile is determined after the first process and a second set of processing parameters are determined. A second process is performed using the second set of processing parameters. Optimizations to improve throughput are also disclosed.