Short answer. Yes. When the building forming part of the property is destroyed, however it happened, the usufructuary may still use the land and the materials. His right shifts to what is left rather than dying with the structure, and that holds even where the usufruct covered the building alone.
What the law says
If the usufruct is constituted on immovable property of which a building forms part, and the latter should be destroyed in any manner whatsoever, the usufructuary shall have a right to make use of the land and the materials.
Civil Code, Article 607 — Destruction of a Building. Read the full provision →
The right survives the structure
The instinct on both sides after a fire or a typhoon is that the usufruct went up with the building. Article 607 says otherwise. The usufructuary keeps a right to make use of the land and the materials — the lot itself and the salvage left on it. Note how little the article cares about the cause: the building may be destroyed in any manner whatsoever, so there is no inquiry into fire, flood, accident or age before the rule applies. The enjoyment simply attaches to what remains.
Even when only the building was given
The harder case is a usufruct constituted over a building alone, where destruction seems to leave nothing that was ever granted. The article extends the same rule there: the usufructuary may still use the land and materials. This is the provision's real work. Without it, a usufruct over a house would be worth exactly as long as the house stood, and the person meant to be provided for — very often a surviving spouse or a parent — would be left with nothing by an event neither party caused.
If the owner wants to rebuild
The owner is not locked out of his own land while the usufruct runs. He may build again, but on terms. The article gives him a right to occupy the land and to make use of the materials, and he is then obliged to pay to the usufructuary, during the continuance of the usufruct, the interest upon the sum equivalent to the value of the land and of the materials. So the usufructuary's enjoyment converts into a periodic money payment measured by what he gave up the use of, running for as long as the usufruct itself would have run. He is compensated, not bought out.
What to establish before the site is cleared
The whole calculation depends on two values: the land and the materials. Both should be fixed while the evidence still exists, which means before the debris is hauled away. Photographs, an inventory of salvage, and an appraisal made at the time are far more persuasive than reconstructions attempted months later. Insurance is a separate question the article does not address, so read the policy to see who is named and what it covers. And where the usufruct was created by deed or will, check first whether that instrument already says what happens on destruction.