Depends on several factors but basically it comes down either to regex, or an ftp mget command.
But really all of your website files should be in one folder, the public_html folder. Or specifically they are not 'website' folders per se.
In that your actual 'website' is in the public_html folder. This is not semantics.
When I backup my site I can do a backup from the root folder, but this isn't necessary as my actual site resides in the public_html. The other folders are default folders. If you enter only the public_html and backup from there, then only that folder will be backed up.
It's a bit like me copying and backing up all my computer files, just to save one email.