Shut down the vm, mount the vm disk, mv the files over, unmount the vm disk, start the vm.

That works because nowadays software doesn’t run itself, the system chooses what to run (sometimes at the users request).

When you shutdown the vm, there is no virtual computer interacting with the files on the vms disk. When you mount the vms disk, you’re just telling your system to treat the file that represents the vms disk as a filesystem. When you move the files to it, you’re just copying the files to the file that represents the vms disk respecting its filesystem then deleting the originals. When you unmount the vms disk you’re telling your system to wrap it up and let go of the file that represents the vms disk. Starting the vm is just telling your system to pretend that it has a fake computer whose disk is that file you mounted and wrote to which just so happens to have some new files in it, imagine that!

There’s another person saying you probably can’t figure out if the files you have are malware. I won’t go that far, but the reason most people don’t setup forensic environments (that’s generally what the computing environment you’ve set up is called when you’re doing what you’re doing) for their warez and instead raw dog it is that they have some security software and process they trust and if they get catch some kind of problem they plan on just restoring from backup.

You do have backups, right?

It’s rare for user targeted malware to have persistence, most of that technology is targeted at infrastructure like switches, edge and servers, so a wipe and restore is almost always a perfect fix.