In the MongoDB configuration file add the following line:
smallfiles=true
The safety shut off MongoDB and remove the journal files.
Full procedure:
sudo cp -p /etc/mongod.conf{,.BAK}
sudo vi /etc/mongod.conf
sudo /etc/init.d/mongod stop
sudo rm -rf /var/lib/mongodb/journal/*
sudo /etc/init.d/mongod start
All the files in /var/lib/mongodb/journal/ are recreated when mongodb starts.
Via: http://lostquery.com/questions/313/how-do-i-shrink-the-mongodb-journal-files