Lasers, electron microscopes and x-ray scanners used for testing and verification in the semiconductor manufacturing industry plus loads of custom and open source tools.
Though even then, you have to have something to compare it with and also know what you are looking at and able to eliminate what should and shouldn't be there.
Though when you have multilayer flash, the possibility to have a nefarious layer, sandwiched between good layers, makes things way harder.
All that said, as a rule, I'd just downright ban any non-company/entity USB drive or any tech. Keyboards and Mice, more so.