Well, if you really need the files saved in a directory, rather than inside the files API (you haven't explained why this is a requirement, but I'll assume for the moment that you have a good reason for doing so), then the following code should work.
$fs = get_file_storage();
$files = $fs->get_area_files($contextid, $component, $filearea, $itemid, 'filename', false);
foreach ($files as $file) {
$file->copy_content_to($destdir.'/'.$file->get_filename()); }
This code assumes you've already used the standard Moodle functions to save the files from the draft area into a known location (although, in theory, you could use the $contextid, $component, $filearea and $itemid of the draft area to do this). If you want to, you could add a $file->delete() call inside the loop to delete the files from the Moodle API at the same time.
I've also assumed you don't want the subdirectories (only the files themselves), so I've passed 'false' as the last param to get_area_files.
