If you have multiple caches for a template, you can clear a specific cache by supplying the cache_id as the second parameter. You can also pass a $compile_id as a third parameter. You can "group" templates together so they can be removed as a group. See the caching section for more information. As an optional fourth parameter, you can supply a minimum age in seconds the cache file must be before it will get cleared.
See also clear_all_cache() and caching.