I want my files to be secure in my web server. Only authenticated users to access those files should be able to access those files. I thought of storing files in database as
A few options come to mind.
If you are using Apache you can use htaccess to password protect directories. (first googled link : http://www.javascriptkit.com/howto/htaccess3.shtml)
or Store the files above the web server. Create a script in php that will allow authorised users to access them.
If you want to do it Via FTP, and you are running cpanel you may be able to create new ftp accounts. check yourdomain.com/cpanel to determine if you have it installed.