A system for separating a solid magnetic substrate from liquid contents of a reaction vessel, the system comprising at least one micro-well plate having a plurality of rows and a plurality of magnets arranged in at least two rows. In one embodiment, the at least two rows of the plurality of magnets are controlled so as to cause the magnets in the at least two rows of magnets to move in unison. In another embodiment, one row of the at least two rows of the plurality of magnets is controlled so as to cause the magnets in said one row to move at a first velocity in the vertical direction and another row of the at least two rows of the plurality of magnets is controlled so as to cause the magnets in that other row to move at a second velocity in the vertical direction.