I am working on DNN 4.05, right now i have to customize the DNN File manager available to dnn host and admin,
whats my requirement is :
I want to display only those folders which have permissions and rest I want to make invisible: like i have this scenario -

In file manager i have below folder structure:-

Portal Root
--- Websites (subfolder of Portal Root)
        --- Mysite1 (subfolder of Website)
        --- Mysite2 (subfolder of Website)
        --- Mysite3 (subfolder of Website)


what i want is i wan to display only Mysite1 and Mysite3, Mysite2 should not be visible.

please let me know if some one can help on this..

Thanks in advance.

each portal will have its own file structure, i.e.

/portals/_default   - host
/portals/0/              - first web site
/portals/1/              - second web site
...

permissions are granted per portal as Stefan poited out before.

don't grant view permission for the folder prevents modules to list it for delivering files using "Linkclick.aspx". to prevent it to be delivered by other modules, you need to declare the folder "secure FileSystem".