Whether it even makes sense to clean infected computers is a topic of repeated heated discussion in the IT security world. Questions such as "Can I ever really trust a computer again once it has been infected?" or "Is it technically possible to completely clean a system?" always come to the forefront of these discussions.

Malware constructed in a simple manner can usually be completely removed from a system with a high level of reliability.

The more complex the Malware, the more difficult the cleaning process. The main problem is that you can never be really sure that the cleaning was completely successful. In many cases the cleaning functions of security products function as placebos that disguise the true facts: The logical conclusion that the PC can no longer be trusted once it has already been infected by Malware.

Do not trust cleaning alone. Protecting the PC against Malware infection in the first place is always better than subsequently attempting to clean up the chaos created by an infection. This means using a multi-layer protection system with real-time protection.

A nice read at Emsisoft Knowledgebase: On the sense and senselessness of Malware cleaning