A molecular arrangement magnetic treatment apparatus and method includes a material container with an inlet and an outlet where the material to be treated is introduced at the inlet and is released at the outlet and where the material container is sized so as to provide an enclosed space into which the material expands and loses velocity. A material passageway is connected at one end to the inlet and at another end to the outlet such that the material must pass through the material passageway. And at least one pair of magnets is provided that are oriented such that material in the passageway must pass between a north pole and a south pole of the pair of magnets. In one embodiment, the at least one pair of magnets is self aligning such that the north pole and the south pole are free to move so that the north pole and the south pole are always facing each other. In another embodiment, a precipitator is connected with the material container and negatively charged material is precipitated from the material after the material has been negatively charged.