Enable Disk Cleanup on Windows Server 2008 / 2008 R2

In order to use cleanmgr.exe you’ll need to copy two files that are already present on the server, cleanmgr.exe and cleanmgr.exe.mui. Use the following table to locate the files for your operating system.

Windows Server 2008 R2 64-bit
C:\Windows\winsxs\amd64_microsoft-windows-cleanmgr_31bf3856ad364e35_6.1.7600.16385_none_c9392808773cd7da\cleanmgr.exe

Windows Server 2008 R2 64-bit
C:\Windows\winsxs\amd64_microsoft-windows-cleanmgr.resources_31bf3856ad364e35_6.1.7600.16385_en-us_b9cb6194b257cc63\cleanmgr.exe.mui

Windows Server 2008 64-bit
C:\Windows\winsxs\amd64_microsoft-windows-cleanmgr.resources_31bf3856ad364e35_6.0.6001.18000_en-us_b9f50b71510436f2\cleanmgr.exe.mui

Windows Server 2008 64-bit
C:\Windows\winsxs\amd64_microsoft-windows-cleanmgr_31bf3856ad364e35_6.0.6001.18000_none_c962d1e515e94269\cleanmgr.exe.mui

Windows Server 2008 32-bit
C:\Windows\winsxs\x86_microsoft-windows-cleanmgr.resources_31bf3856ad364e35_6.0.6001.18000_en-us_5dd66fed98a6c5bc\cleanmgr.exe.mui

Windows Server 2008 32-bit
C:\Windows\winsxs\x86_microsoft-windows-cleanmgr_31bf3856ad364e35_6.0.6001.18000_none_6d4436615d8bd133\cleanmgr.exe

Once you’ve located the files move them to the following locations:
Cleanmgr.exe should go in %systemroot%\System32.
Cleanmgr.exe.mui should go in %systemroot%\System32\en-US.

You can now launch the Disk cleanup tool by running Cleanmgr.exe from the command prompt.
Disk Cleanup can now be run by entering Cleanmgr.exe into a command prompt, or by clicking Start and typing Cleanmgr into the Search bar.

https://technet.microsoft.com/en-us/library/ff630161(WS.10).aspx