Microsoft requires that the Desktop Experience feature be installed on Server 2008 R2 for the Disk Cleanup Utility to work, but you can work around that requirement.
Start a Command Prompt running as Administrator and run the following:
copy C:\Windows\winsxs\amd64_microsoft-windows-cleanmgr_31bf3856ad364e35_6.1.7600.16385_none_c9392808773cd7da\cleanmgr.exe c:\windows\system32 copy C:\Windows\winsxs\amd64_microsoft-windows-cleanmgr.resources_31bf3856ad364e35_6.1.7600.16385_en-us_b9cb6194b257cc63\cleanmgr.exe.mui c:\windows\System32\en-US cleanmgr.exe
Microsoft Article: https://technet.microsoft.com/en-us/library/ff630161(v=ws.10).aspx