How to clean up my external drive?

First, there is no reason to ever install or run any 3rd party "cleaning", "optimizing", "speed-up", anti-virus, VPN or security apps on your Mac.  This documents describe what you need to know and do in order to protect your Mac: Effective defenses against malware and other threats - Apple Community and Recognize and avoid phishing messages, phony support calls, and other scams - Apple Support.  

There are no known viruses, i.e. self propagating, for Macs.  There are, however, adware and malware which require the user to install although unwittingly most of the time thru sneaky links, etc.   

Anti Virus developers try to group all types as viruses into their ad campaigns of fear.  They do a poor job of the detecting and isolating the adware and malware.  Since there are no viruses these apps use up a lot of system resources searching for what is non-existent and adversely affect system and app performance.

There is one app, Malwarebytes, which was developed by a long time contributor to these forums and a highly respected member of the computer security community, that is designed solely to seek out adware and known malware and remove it.  The free version is more than adequate for most users.  

That being said I strongly suggest you uninstall CleanMyMac according to the developers instructions, CMM is considered by many here to be akin to malware.

You can check to see if you've removed all of the supporting files by downloading and running the shareware app Find Any File to search for any files with the application's or the developer's name in the file name.  For CMM software you'd do the following search(es): 

1 - Name contains cleanmymac

2 - Name contains macpaw

Any files that are found can be dragged from the search results window to the Desktop or Trash bin in the Dock for deletion.

FAF can search areas that Spotlight can't like invisible folders, system folders and packages.  

If you get warnings that the file can't be deleted because it is in use or used by another app boot into Safe Mode according to How to use safe mode on your Mac and delete from there.

Note:  if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode.  This makes it act as a wired keyboard as will assure a successful boot into Safe Mode.02

Get rid of cleanmymac. Its malware. And what do you mean by "Clean up my drive"?

If the backup disk is a Time Machine disk you can't delete them from that drive. It's a read only drive except for Time Machine. So remove them from the boot drive and leave the TM drive alone