In each level of the Pharos subterra there are rooms to the NW, NE, SW and SE with pedestals in them, most of which join onto other rooms with monsters in. You basically have to kill these monsters for black orbs and place them on each pedestal. Once each pedestal is "fully activated", the elevator will take you to the next floor of the subterra.

The correct amount for each pedestal (in the order NE, NW, SE, SW) is as follows:

Penumbra : 18, 9, 3, 6
Umbra: 15, 9, 15, 18
Abyssal: 15, 21, 27, 12

The first monster you kill upon entering a room adjoining a pedestal room will drop a black orb, every 3rd monster thereafter will drop one. Any black orbs you miss go to a "massive black orb" that can contain really large amounts of normal black orbs.