Can't see certain folders

I'm a new admin running Server 2008R2 on Cisco hardware. A user created a subfolder and wanted special permissions for that folder. I accessed the Server Desktop, went to "computer" to look for that folder and noticed that I can't locate it.
There are several folders that I can see if I'm looking on the file server itself (I access via a VPN) but I can't see these folders in such a way that I can set permissions. Any help would be greatly appreciated.

You need to contact your user to provide you that path where he created the folders. You can also use them using Windows Explorer: Of course, results might take long time to be shown if indexation is disabled.
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