I don't know the specifics but I imagine most of it is waving a magic wand and saying poof now this room is classified. But there are logistics that go with that, certain door technologies that have to be in place, probably some complex security procedure for "switching" between modes, (i.e. I would think they need to clear the building of uncleared personnel and be 100% sure there isn't someone hiding in a bathroom somewhere) etc etc, and it's enough of a pain that most buildings are either one or the other all the time. The ability to switch on the fly for a large facility like that is super rare and indicative of there being a real need for switching.

All I know for sure is on the tour they mention they can switch the whole building to be unclassified or classified and during the tour it is in unclassified mode.

I've heard that, at an air force base where civilians work, there's a blue light that turns on both on the door and inside the room, when that room is in "classified" mode, and they are only allowed to do classified work when the light is on and the door closed.

To be clear though, I don't think anything about NIF's actual design is classified. Maybe the parameters they use on some tests and the angles on some of the lenses and/or target design/composition are, but the actual setup is all publicly documented AFAIK.

The aliens have to go to their cryopods :).