Ok I have a little more information here. It turns out that the 3 default "FTP" definitions do not enum in the ProtocolDefinition Collections. I believe this is because they are defined by an Application Filter not the ISA Server. So, basicaly what I need help doing is adding elements of an application filter to a Protocol Rule Set. It is rather anoying to be able to add it through the GUI with the click of a button but cant seem to get at it in code.