ok, im a huge rage against the machine fan and i knwo all tom morrelo's tricks and this is one. The song you heard was probably "voice of the voiceless" off the battle of los Angeles album, track nine.
fist, get yourself a Digitech Whammy pedal, any version will do, but i like the whammy 2, the same one that tom morrello has,(theres not that much difference between them so it doesnt matter)
second, get a little familiar with the pedal, mess with the expression pedal and the selector knob.

finaly, turn on the Whammy Pedal, play one note and keep it continuouse, play quarternotes or somethign, i like to play an open G. manipulate the knob keeping it in the harmonizer section of the pedal's range. if that dont give you the sound ya want then you are a lost cause my friend

hope that solved it!