The easiest thing to do is to use your hosting company's control panel (cPanel, Plesk, etc) file utility to move all your subdirectory's files and folders to up to your web root. (If you're comfortable using the command line you can always do that instead...)

Then take a look at (your_site_root)/config/site.php and if there's a BASE_URL setting defined, delete that line.

Using FTP to move files & folders is a bad idea because the FTP protocol opens a new connection for each file it moves. If one of these fails, a file can get "left behind" and that can cause problems.

Hope that helps!