I don't know of a naturally tree-structured language (setting aside XSLT, which isn't a general purpose language), though maybe Prolog would qualify.
Why not Lisp as a "naturally tree-structured language"?
Lists are constructed and destructured really as trees, less frequently as flat, single level lists. From list pattern matching down to the traditional list primitives (car, cdr, caar, cadr, ..., cdddar, cddddr), Lisp and lists have been manipulating trees.
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