SharePoint Diagnostic Manager initially identifies all servers associated with a farm, as described by Central Administration, to make the process of registering farm servers easier. This may result in some non-WFE servers in the environment (e.g. email servers) being counted against farm servers for licensing purposes.
In the event that such servers do not have to be monitored, navigate to Options > Manage Licenses and uncheck the servers in question. This will disable the server from monitoring, but it will still show up in the list of servers. Currently, there is no way to remove a server from the left-most topology list.