First of all, ensure that media server to be deleted has been decommissioned properly. You will find a link under 'featured discussions' that describes the new decommissioning tool.
There are also numerous posts on this forum as well as TechNotes on how to decommission media servers.
The last step in this process is to delete the hostname from EMM:
nbemmcmd -deletehost -machinename <string> -machinetype <api | app_cluster | client | cluster | disk_array | master | media | ndmp | virtual_machine>