You can purchase a good package that would do the monitoring for you and then initiate whatever process that you want to do on the AS400 or other server. I highly recommend GoAnywhere from Linoma Software.
We used to have a process that would kick off every 5 minutes and create FTP commands on the fly. The first one would do an LS command to create a list of the files on the server. Then we read that in to determine what files are currently on the server and then create another FTP process to pull the file, process it and then delete it from the server.