1. Go to the particular message that includes the variant you would like to remove
  2. Select delete under action.
  3. It will open a page of all variants and you can select which version you would like to remove.  If it does not have a variant it will delete the only version.
*Important to note, you cannot delete messages that have been sent, or if there was an audience generated and the message was cancelled.  Attempting to delete messages that have been sent will result in an error message.  You can archive these messages to hide them from the view of messages, but archived messages will not appear in some reports.