In the article OP linked I found this section :

Archaeologists preserved the newly discovered remains using a variation of a technique developed by Italian archaeologist Giuseppe Fiorelli in 1863. The process involves pouring liquid chalk into cavities left by decomposing bodies; this plaster fills gaps in preserved bones and teeth, creating a cast of the bodies as they looked at the moment of death.

So you find a cavity with bones and other remains in there and use it as a mold I suppose? They probably were excavating the city from the ash cover and when they found something that could be remains of a human they stopped digging and used said techniques to preserve the remains.