Disinfect File

So we can inject the payload in a file as a nwe thread right?? So that the file works normally but the payload works its magic too right??

So.. Question 1

If I have a file that I know is infected with a payload or virus... how do I disinfect the file so that the file works as it should but the payload/virus gets removed??

Question 2

If I put a reverse-https or some sort of exploit in a file as a new thread... and make the file run as administrator... will then it will still ask the user to allow the connection for the reverse-https??