FTP protocol does not provide a way to directly access or change a file on a server.

When you edit a file whats really happening is your downloading the file, editing it, and then replacing the file through a file delete followed by an upload.

So the only way would be to download files, scan them and then delete or replace any infected files.

I think you will find thats how any AV that claims to scan FTP works, unlike a TCP/IP network connection, FTP does not provide a way to "remotely do things on a servers hard drive"

Right click and scan a very large file on the FTP and you'll see by the time it takes that a download happens first.

Compare the time to a scan of the same file already on your system.

Dave