Windows Server Operatin Systems by default do not have Disk Cleanup enabled. Here are the steps to get them enabled on Windows Server 2008 R2:
Find the following files:
C:\Windows\winsxs\amd64_microsoft-windows-cleanmgr_31bf3856ad364e35_6.1.7600.16385_none_c9392808773cd7da\cleanmgr.exe
C:\Windows\winsxs\amd64_microsoft-windows-cleanmgr.resources_31bf3856ad364e35_6.1.7600.16385_en-us_b9cb6194b257cc63\cleanmgr.exe.mui
Once you’ve located the files move them to the following locations:
Copy Cleanmgr.exe to %systemroot%\System32.
Copy Cleanmgr.exe.mui to %systemroot%\System32\en-US.
You will now be able to open Disk Cleanup you can use Windows Run (cleanmgr.exe)