In a nutshell, Lucene builds an inverted index using Skip-Lists on disk, and then loads a mapping for the indexed terms into memory using a Finite State Transducer (FST). Note, however, that Lucene does not (necessarily) load all indexed terms to RAM, as described by Michael McCandless, the author of Lucene’s indexing system himself. Note that by using Skip-Lists, the index can be traversed from one hit to another, making things like set and, particularly, range queries possible (much like B-Trees). And the Wikipedia entry on indexing Skip-Lists also explains why Lucene’s Skip-List implementation is called a multi-level Skip-List – essentially, to make O(log n) look-ups possible (again, much like B-Trees).
So once the inverted (term) index – which is based on a Skip-List data structure – is built from the documents, the index is stored on disk. Lucene then loads (as already said: possibly, only some of) those terms into a Finite State Transducer, in an FST implementation loosely inspired by Morfologick.
Michael McCandless (also) does a pretty good and terse job of explaining how and why Lucene uses a (minimal acyclic) FST to index the terms Lucene stores in memory, essentially as a SortedMap<ByteSequence,SomeOutput>, and gives a basic idea for how FSTs work (i.e., how the FST compacts the byte sequences [i.e., the indexed terms] to make the memory use of this mapping grow sub-linear). And he points to the paper that describes the particular FST algorithm Lucene uses, too.
For those curious why Lucene uses Skip-Lists, while most databases use (B+)- and/or (B)-Trees, take a look at the right SO answer regarding this question (Skip-Lists vs. B-Trees). That answer gives a pretty good, deep explanation – essentially, not so much make concurrent updates of the index “more amenable” (because you can decide to not re-balance a B-Tree immediately, thereby gaining about the same concurrent performance as a Skip-List), but rather, Skip-Lists save you from having to work on the (delayed or not) balancing operation (ultimately) needed by B-Trees (In fact, as the answer shows/references, there is probably very little performance difference between B-Trees and [multi-level] Skip-Lists, if either are “done right.”)