Some malware is so invasive that complete removal is unlikely. Its like a hydra, you remove parts of it and it creates more. This is why you could always backup data and have a clean image of your operating system or at the very least a way of reinstalling the operating system.
Much of this type of malware is randomly generated. You are wasting your time if you've already spend more than 1 day trying to clean the system. The patient has terminal cancer and you are using antibiotics.
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Most antivirus applications are preventative measures, and aren't great at actually cleaning the system of malware. They work by monitoring the system for unusual processes, however if you are already infected they are too 'slow' to work.