Enter the RMT PWNER program, version 1.337. (No, we totally did not make that up.) This program can parse the many servers of FFXI for information regarding the buying and selling transactions of a character under suspicion of the task force. The program will then list all characters who have associated with that character's associates, and so on and so on. This way, the task force will be able to easily track all members of a supposed RMT group without doing all of the human legwork of tracking through endless log files.
In addition, the team is implementing "The Guilded Tomb," a tool that performs quick lockdown of a character's account if the suspicious character carries too much gil at one time, and the magical "Auto-Jailer," a program that will run in the background of all servers and throw suspicious players into Vana'diel's jail once they have met a certain criteria.
While these tools need to be tested in the field to see exactly how well they will perform, it only speaks to how aggressively Square-Enix attempts to shut down the sale of currency for real money in their world -- especially when you have players that feel just as strongly about stopping RMT as the company itself.