Can you show us recover command you used? I never saw this "directory is not empty" thing before and may indicate some sort of permission or recover setting issue.... Is data saved as data belonging to application server or mount server?

I am using backup and recovery GUI
the data that is being recovered is Exchange server storage group.
We take backup of clone which is mounted on mout server.
I m trying to restore this clone data on mount server itself which are some directories.

OK, let me see if I get this correctly...

You have application host - let's call it appl.box. You have EXCH db on it and you take clone of it (I assume CLARiiON clone). This clone in mounted on mount machine - let's call it mount.box. Once mounted you run backup of it as flat file backup on mount.box. Am I correct here?

Now, you wish to restore those files you've been backing up, right? First, since I assume you are restoring whole clone here, can you confirm you wish to restore whole clone mounting point? If so, simply run ssid recover - it will make things much easier and faster. If not, let us know....