Label your tools in a way that identifies them as belonging to you or your department. If one goes missing or is found by another person, it will be easier to trace ownership back to you. If a bar-code or electronic identification system is available, use it. If not, etch your name or your department's name onto each tool.
If you bring an entire tool box into a FOD area, consider taking a photograph of the interior. This documents which tools you took or did not take with you into the area. Then, when you leave the area, you or an inspector can quickly confirm that all tools that entered the area did indeed exit the area.
When using a tool, consider attaching a tether or lanyard to it, then securing the other end to yourself or a stationary object. This especially comes in handy when the tool might fall into a deep compartment beyond reach, or when other personnel might walk away with your tool without your permission. Also keep track of your tethers and fasteners as individual objects, so that they do not themselves become FOD.
Your facility may also have formal tool check-in / check-out procedures. Follow them.
