Rocks and stones are everywhere in A Canticle for Leibowitz. We imagine the complete and total destruction of the world would leave you with a surplus of rubble. But the novel doesn't contain references to rocks and stones just to make the novel's wasteland more believable, or to maintain the nuclear holocaust feng shui.
Here are a couple of the more meaningful appearances of rocks and stones in the novel:
Francis is building a shelter out of rocks when the wanderer meets him. It's noted that the rocks he's using are from the ruins of the last civilization, and that "human erosion had all but obliterated [their] resemblance to buildings" (1.72).
In Fiat Lux, the soldiers and Thon Taddeo take detailed measurements of the stone walls of the abbey. Dom Paulo also references how the abbey's walls are thick to provide sanctuary for any philosopher seeking it (22.130).
When the nuclear blast hits, Zerchi is caught in the destroyed abbey, leaving him buried beneath "[f]ive tons of rock" (29.42).
Of course, this list is far from complete, but these examples serve our primary point. Among other things, rocks and stones symbolize the cyclic nature of time. The rocks Francis uses to build his shelter come from the buildings of the previous civilization.
Later, the Leibowitz Abbey builds thick walls from these stones, showing the beginnings of another civilization. But this civilization comes to be destroyed by nuclear weapons as well, and the same thick walls Dom Paulo bragged about bury and kill the new abbot.
The stones return to the earth and bring Zerchi with them.
The question remains though: will Rachel use these stones to build a shelter as Brother Francis once did? Guess we'll have to read the sequel to find out. Wait, there is no sequel. Aw, shucks.