Hi Music,
The method depends entirely on the type and severity of the infection. With very serious infections, a fix requires several different steps/methods using lots of different software. Unfortunately, the fact is there isn't a single method that will fix everything, with the exception of a format/install.
Some infections are relatively easy to remove using a single tool such as MSE, Norton, AVAST, Comodo, NOD (nominate your favorite anti-malware software here). Everyone has their favorite, so I have learn't to never ask "which is the best anti-malware software" : you will come away more confused than when you started.
Other infections might be more difficult, for example some rootkits. Some require a significant amount of work - visit a malware forum and watch people being helped to remove something very serious : its a long, arduous and time consuming exercise involving many steps with several tools that most of us have never even heard of.
Many people, including respected security experts here, advocate that the only way to be completely sure that an infection has been removed, is to wipe/format the disk and do a clean install. This is especially important in the case of the more severe infections that are known to steal and pass on personal information to other computers.
Regards,
Golden