No way to do it if the machine is compromised.
Doesn’t Malware Bytes detect these things?
He’s right. There is no way to have any confidence in anything now running on this machine. Although you can save your documents and such, I would scan any content you pull from the compromised machine on an entirely different computer. [In fact, I would scan it with two different virus scanners if it was one of my clients.] Just because a file isn’t an “executable” that doesn’t mean you can’t be tricked into opening it in a way that re-installs malicious code, so even supposedly “safe” content has to be approached as if it’s compromised until proven otherwise.