Ouch, I don't want to disillusion you, but this can be a very ungrateful job.

Time-consuming and often unsatisfactory results.

I usually reinstalled the system after a complete data backup and configured it as securely as possible. The latter is actually the most important part.

And you should always have an emergency system ready. Linux on a USB stick is best in my experience...

And yes, it comes with a built in scanner but this doesn't do it's job properly an many cases.