Sure. I'll give you the generic process in a secondary environment.
Let's say it's at the airport. An individual who's travelling is sent, based on indicators, to secondary for an examination. Sometimes they're sent to secondary just for paperwork, to pay their duties and taxes. In this case, let's say the indicators say there's non-compliance. During the process of the examination, the officer will use non-intrusive tools before they go to a more intrusive search. If they started with the X-ray, they'll also use the ion scan device. They can use density meters. They can use a number of tools to help build those indicators before they move to more progressive or intrusive examinations.
To your question about the ion scan and how they use it, the officer who is trained will take the swab, make sure the swab is clean, and swab an area, perhaps a suitcase. They will then take the swab back to the machine and reinsert it to check for a reading.