Brake Pad bedding / Rotor deposits

[Larry Herman]

Chris is pretty much correct here.  It is usually an incompatibility of brake materials that can lead to your problem.  If it is not that deep, cleaning it off may work.  You can use something more aggressive than a scotchbrite pad.  Another thing that can occur is crystallization of the rotor metal due to material induced hot spots.  If that happens you usually wind up replacing them.  Cutting the rotor should fix it if it has enough thickness left.