Objection 1. It would seem that neither will all the elements be cleansed by that fire. Because that fire, as stated already (3), will not rise higher than the waters of the deluge. But the waters of the deluge did not reach to the sphere of fire. Therefore neither will the element of fire be cleansed by the final cleansing.
Objection 2. Further, a gloss on Apocalypse 21:1, "I saw a new heaven," etc., says: "There can be no doubt that the transformation of the air and earth will be caused by fire; but it is doubtful about water, since it is believed to have the power of cleansing itself." Therefore at least it is uncertain that all the elements will be cleansed.
Objection 3. Further, a place where there is an everlasting stain is never cleansed. Now there will always be a stain in hell. Since, then, hell is situated among the elements, it would seem that the elements will not be wholly cleansed.
Objection 4. Further, the earthly paradise is situated on the earth. Yet it will not be cleansed by fire, since not even the waters of the deluge reached it, as Bede says (Hexaem. i, ad Gen. 2:8), as is stated in Sentent. ii, D, 7. Therefore it would seem that the elements will not all be wholly cleansed.
On the contrary, The gloss quoted above (5, Objection 1) on 2 Peter 3:12 declares that "this fire will engulf the four elements."
I answer that, Some [St. Bonaventure, Sentent. iv, D, 47, 2, 3] say that the fire in question will rise to the summit of the space containing the four elements: so that the elements would be entirely cleansed both from the stain of sin by which also the higher parts of the elements were infected (as instanced by the smoke of idolatry which stained the higher regions), and again from corruption, since the elements are corruptible in all their parts. But this opinion is opposed to the authority of Scripture, because it is written (2 Peter 3:7) that those heavens are "kept in store unto fire," which were cleansed by water; and Augustine says (De Civ. Dei xx, 18) that "the same world which perished in the deluge is reserved unto fire." Now it is clear that the waters of the deluge did not rise to the summit of the space occupied by the elements, but only 15 cubits above the mountain tops; and moreover it is known that vapors or any smoke whatever rising from the earth cannot pierce the entire sphere of fire so as to reach its summit; and so the stain of sin did not reach the aforesaid space. Nor can the elements be cleansed from corruptibility by the removal of something that might be consumed by fire: whereas it will be possible for the impurities of the elements arising from their mingling together to be consumed by fire. And these impurities are chiefly round about the earth as far as the middle of the air: wherefore the fire of the final conflagration will cleanse up to that point, since the waters of the deluge rose to a height which can be approximately calculated from the height of the mountains which they surpassed in a fixed measure.
We therefore grant the First Objection.
Reply to Objection 2. The reason for doubt is expressed in the gloss, because, to wit, water is believed to have in itself the power of cleansing, yet not such a power as will be competent to the future state, as stated above (5;k22, ad 2).
Reply to Objection 3. The purpose of this cleansing will be chiefly to remove all imperfection from the abode of the saints; and consequently in this cleansing all that is foul will be brought together to the place of the damned: so hell will not be cleansed, and the dregs of the whole earth will be brought thither, according to Psalm 74:9, "The dregs thereof are not emptied, all the sinners of the earth shall drink."
Reply to Objection 4. Although the sin of the first man was committed in the earthly paradise, this is not the place of sinners, as neither is the empyrean heaven: since from both places man and devil were expelled forthwith after their sin. Consequently that place needs no cleansing.
Source: Summa Theologica (New Advent)