[Need Help] Directory Permissions

Hey guys, I am currently working on a project where a user on a site can upload files and also download files. I only want certain users to have viewing capabilities of certain directories. All of the files that are uploaded are stored in a mysql database and can be downloaded from there as well. Does anyone have any idea how to make it so that certain users can only see a specific directory or have access to only their directory? All of the users are stored in a mysql database as well and each user has their own unique user id.

Maybe by putting the files outside the webroot. Than once a user is logged in he has access to a script that reads the file?
http://php.net/manual/en/function.readfile.php