Cleaning or otherwise removing a virus infection is referred to as disinfection. In some instances, an infection cannot be disinfected and the file must simply be deleted. For example, a Trojan would always be deleted as it has no legitmate purpose. Conversely, a document infected with a macro virus would be cleaned. That is, the offending macro(s) would be removed while the document, and any non-infected macros, would be left intact.
While disinfection can generally be accomplished with no resulting file damage, there is no absolute guarantee that the file can be restored to its original state. For this reason, some antivirus experts recommend always restoring infected files from a known clean backup, and relying on antivirus software only to detect the virus.
Other antivirus experts believe disinfection is the preferred method, rather than requiring the user to have (a) made a backup, and (b) to restore it. Some independent testing facilities certify antivirus software on its ability not just to detect viruses, but also their accuracy in disinfecting them.
In many cases, cleaning or disinfecting is not a viable option. To understand the distinctions, see Clean, Quarantine, or Delete.