1) Delete all websites, mail domains and dns zones that belong to the server which shall be removed. Wait until the jobqueue has cleared. This will remove the items inside ispconfig and on the slave server. This has to be done on traditional server setups, not mirroring setups!
2) Login to the slave server and remove the server.sh cronjob from root crontab.
4) Delete the record of this server in the "server" database table of the ispconfig DB on the master.