The software is called DMS Shuttle and it works great for deleting past versions from SharePoint. As of this writing Microsoft only allows you to put a minimum of 100 versions on a file/library. That adds up quick so I use this tool to free up cloud storage.

DMS-Shuttle: File Migration Tool for SharePoint Online, 2010, 2013, 2016

Open the DMS Shuttle program then click the folder icon. For this example, I will select my saved connection and click Open
I won’t go through how to setup a new connection, but it was straight forward, and you do that by clicking New and completing the wizard.

Use the below numbers to see what steps to take in the picture.

  1. Select a SharePoint Site (Sales in this example) 
  2. Right click the target Document Library (Customers in this example) 
  3. Select Bulk Operations 
  4. Click Bulk Delete Version History 

It will then do this for a while to gather how many items are in the list 

Once that is done you will be presented with a prompt to enter how many versions you want to keep. I normally leave it at 3 then click OK 

You can see the progress in the below window of the program: