Hello,
I don't think there is a way to do that built in. You see, when a file is being used, that's not information that's saved in the database unless it is being used by a block. But then you would need to know what blocks you are using that are using files from the manager and then deal with each separately.

Another way would be to totally turn off the cache so the site uses files directly and not from the cache, then use a crawler to crawl your site and find out about all files that come from the "files" folder.

Anything I can think of is really a hack though so probably not worth the time.