The cylinders were carried by the ghoul and zombies at the signalling device.
The cylinder carried by the ghoul gave access to the tower underneath the device via a secret door and those carried by the zombies gave access to doors within the tower. It also looks like those carried by the zombies will fit into the holes around the hexagram in the inner room of the tower.
The 5, 6-pointed cylinders were placed in to the slots at the points of the hexagram and one empty slot remains.
On the way out of the tower, Mahgnim Rib threw the 5 pointed cylinder back through the door which promptly slammed shut and preventing further access.