FTP server has been tagged

One of my ftp servers has been “Scanned and Tagged”!
Recently we had all new Cisco router/firewall installed, two days later my MS-IIS FTP server got tagged. (Didn’t take “them” long did it?!) Now there are several directories which I can not delete completely. So my questions are – What is it? How did they get in? How do I get rid it, and how do I protect from future attacks?

V/R
Dave Leonard