Step 1: Open Microsoft Outlook (this process will work in versions 2013 and 2016).
Step 2: Select the folder in which the duplicate emails are.
Step 3: Under Home, select the Clean up drop down box in the Ribbon.
Step 4: Select Clean up conversation to delete and move duplicate emails in the conversation to the Deleted Items folder.
Step 5: Click on Clean up folder to delete and move duplicate emails in the specific folder to the Deleted Item.
Step 6: The clean up folder and sub folders will allow you to clean up also subfolders.