My PC got bugged with a very elusive trojan horse. It spams pop-ups for virus removal tools etc.

With past infections, I was usually able to locate the suspect executable file and delete it in safe mode.

In this case, I ran Spyware Doctor which detected the trojan horse (7 files in the registry). I selected fix and it said that it removed the threats, but when I ran it again they were still there.

What can I do now to remove this trojan horse?

Download and install malwarebytes, you can use it as free and no need to purchase

Let it 'fix' whatever it finds and hope it gets it
Malwarebytes.org