If a virus is found & announced when you start an application or when you open a file e.g. in Notepad (technically, when scanning the file "on execute" or "on open"), the virus warning is given before the file is really started/accessed and the access is denied - so you don't have to worry about the infection. The virus is not allowed to launch.
The only exception is scanning the "created/modified files" (disabled by default) - in this case, the warning is given after the file has been actually infected (technically, it's scanned on "close") - but it can't be done in any other way. However, according to what you write, it's not your case.