
In Windows 8.1 the File Explorer now has a panel called “Folders” that contains shortcuts to six of the most common user folders:

To remove these folders we need to edit the registry.
From the desktop press the Windows + R keys together to open the Run dialogue box. Type regedit and then press the Enter key. Navigate to the following registry key:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\

As we can see the NameSpace subkey contains six GUIDs which are mapped to the user folders as follows:
{1CF1260C-4DD0-4ebb-811F-33C572699FDE} - Music Folder
{374DE290-123F-4565-9164-39C4925E467B} - Downloads Folder
{3ADD1653-EB32-4cb0-BBD7-DFA0ABB5ACCA} - Pictures Folder
{A0953C92-50DC-43bf-BE83-3742FED03C9C} - Videos Folder
{A8CDFF1C-4878-43be-B5FD-F8091C1C60D0} - Documents Folder
{B4BFCC3A-DB2C-424C-B029-7FE99A87C641} - Desktop Folder
Deleting all of these GUIDs from the NameSpace folder will remove these folders from Windows File Explorer:

On Windows 8.1 x64 this will still leave the user folders visible in the saveĀ / open dialogue boxes:

To remove the user folders from the save / open dialogue box we need to delete the same GUIDs from the following subkey:
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\
This process is easily automated by exporting the required keys and saving them as .reg files.
Remove Folders From File Explorer in Windows 8.1 x64:
Windows Registry Editor Version 5.00
; ####################################################
; Remove Folders from File Explorer in Windows 8.1 x64
; ####################################################
[-HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{1CF1260C-4DD0-4ebb-811F-33C572699FDE}]
[-HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{1CF1260C-4DD0-4ebb-811F-33C572699FDE}]
; Music Folder
[-HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{374DE290-123F-4565-9164-39C4925E467B}]
[-HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{374DE290-123F-4565-9164-39C4925E467B}]
; Downloads Folder
[-HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{3ADD1653-EB32-4cb0-BBD7-DFA0ABB5ACCA}]
[-HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{3ADD1653-EB32-4cb0-BBD7-DFA0ABB5ACCA}]
; Pictures Folder
[-HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{A0953C92-50DC-43bf-BE83-3742FED03C9C}]
[-HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{A0953C92-50DC-43bf-BE83-3742FED03C9C}]
; Videos Folder
[-HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{A8CDFF1C-4878-43be-B5FD-F8091C1C60D0}]
[-HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{A8CDFF1C-4878-43be-B5FD-F8091C1C60D0}]
; Documents Folder
[-HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{B4BFCC3A-DB2C-424C-B029-7FE99A87C641}]
[-HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{B4BFCC3A-DB2C-424C-B029-7FE99A87C641}]
; Desktop Folder
Restore Folders From File Explorer in Windows 8.1 x64:
Windows Registry Editor Version 5.00
; ####################################################
; Restore Folders from File Explorer in Windows 8.1 x64
; ####################################################
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{1CF1260C-4DD0-4ebb-811F-33C572699FDE}]
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{1CF1260C-4DD0-4ebb-811F-33C572699FDE}]
; Music Folder
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{374DE290-123F-4565-9164-39C4925E467B}]
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{374DE290-123F-4565-9164-39C4925E467B}]
; Downloads Folder
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{3ADD1653-EB32-4cb0-BBD7-DFA0ABB5ACCA}]
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{3ADD1653-EB32-4cb0-BBD7-DFA0ABB5ACCA}]
; Pictures Folder
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{A0953C92-50DC-43bf-BE83-3742FED03C9C}]
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{A0953C92-50DC-43bf-BE83-3742FED03C9C}]
; Videos Folder
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{A8CDFF1C-4878-43be-B5FD-F8091C1C60D0}]
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{A8CDFF1C-4878-43be-B5FD-F8091C1C60D0}]
; Documents Folder
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{B4BFCC3A-DB2C-424C-B029-7FE99A87C641}]
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\NameSpace\{B4BFCC3A-DB2C-424C-B029-7FE99A87C641}]
; Desktop Folder
Sources: http://www.howtogeek.com/168081/how-to-remove-the-folders-from-my-computer-in-windows-8.1/