If the path to your public_html folder (the folder in which your host will have told you to upload all files into so that they can be accessed via url)
is for example:

/home/yoursite/public_html/

And when you have setup the clients folder when the File Manager was installed, you entered the directory path in the Configuration.pl file as:

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####Main Clients Directory#####################################################
 
clientroot "/home/yoursite/public_html/FileManager/Clients"
#Change the path to the "Main Clients Directory" to your servers path to the
#main public root directory + the sub-folder of the File Manager folder which 
#will hold all your Clients folders.
#For example:
#e.g.clientroot "/home/yoursite/public_html/FileManager/Clients"
 
###############################################################################

Try setting up a new Clients Folder in the following location:

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####Main Clients Directory#####################################################
 
clientroot "/home/yoursite/Clients"
#Change the path to the "Main Clients Directory" to your servers path to the
#main public root directory + the sub-folder of the File Manager folder which 
#will hold all your Clients folders.
#For example:
#e.g.clientroot "/home/yoursite/Clients"
 
###############################################################################

This way the folder will be outside of the public_html folder and therefore you will be unable to enter a url and locate the files in the Clients folder.

Only access will be granted via the File Manager, which work with paths and not urls's.

You will then need to modify this path on line 104 of the Configuration.pl file.

The second option you can try is setting up an .htaccess file to protect over direct access to the files.

This htaccess password needs to be located in the "Clients" folder.

Advice on how to setup the .htaccess and .htpasswd files can be found here:

http://webdesign.about.com/od/htaccess/ht/hthtaccess.htm

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