Traditional approaches to navigation in focused ion beam (FIB) circuit edit include blind CAD navigation based on GDSII data from the manufacturer and navigation assisted by the in-situ optical microscope (OM). These approaches are difficult to apply in security audit and reverse engineering fields, where CAD data are unavailable and objects of interest are either too small, or located in an array that is too dense for imaging by in-situ OM. To address this issue, this article presents a methodology which is based on establishing a chip-specific system of coordinates and determination of precise locations of the objects of interest within the device. The work was performed on a Vectra 986 FIB system from FEI Company and a proprietary system for optical scanning of semiconductor devices. Auxiliary techniques allowing enhancement of navigational accuracy, developed for this application, are equally applicable to the general navigation procedures during generic FIB circuit modification.