I guess you could try to use the Export Archive Wizard and choose the folder you want removed and also choose the option to delete the items after export.

Details on Exporting a portion of an Archive using the PST Export wizard.

Also, don't forget this:

How to remove the empty folders from Archive Explorer in Enterprise Vault (EV) for Microsoft Exchange

I know there was an issue that hit quite heavy in EV8 where a \SubFolder1 said its parent was \MyFolder, and \myFolder said its parent was \SubFolder1 causing an infinite loop, and Symantec has a tool for repairing them, so you may just want to contact support as it may be a bigger issue..... if its even the same thing, because I wouldn't expect ArchiveExplorer to display anything at that point

So I chose to delete items in this subfolder path "\Deleted Items\" As per the instructions in the article this should delete all folders and their content under "Deleted Items" but not archived emails in the root of "Deleted Items"?

It will export and delete the items in the Deleted Items folder and sub-folders. You will need to use the reg key to delete the empty folders.

You would need to run the process multiple times to get all the items removed and then run the process to remove the empty folders.

I would recommend following JW3's advise about contacting support to make sure you are not affected by the previous issue that he mentioned.

I found the tool RemEmptyFolders written by Rob Wilcox. But I do not understand how to run it.

http://www.symantec.com/connect/downloads/empty-folder-deleter

That is for empty folders in the Vault Store Partition and will not help you with your issue.

TS

But all of the folders in the picture attachment are empty

Yeah but what that script you're referencing does is remove empty physical folders on an EV Partition where the DVS files are held

like

V:\Enterprise Vault Stores\VaultStore1\Ptn1\2014\01-01\A\12\

If that folder is empty, then it deletes the folder, can help in some circumstances where file performance is impacted by enumurating empty folders

However what you have is empty archive folders which is entirely different and not covered by that utility

oh, I'm, sorry, I thought it removed empty folders from archives. So i guess my only option is the registry edit that described in http://www.symantec.com/docs/TECH47918

the export did not remove the folders.