A motor drive system for use with a motor comprising a first high-side switch coupled to a high voltage bus and the motor. A first low-side switch coupled to the motor and a return, a turn ON and turn OFF of the first high-side switch and the first low-side switch provides a phase current for the motor. A system controller configured to receive a phase current sense signal representative of the phase current of the motor and configured to begin an alignment sequence to align the motor to a goal alignment position, wherein during the alignment sequence at least one of the first high-side switch or the first low-side switch is turned ON and OFF having an alignment duty ratio, and the system controller is configured to end the alignment sequence in response to a sensed decrease in the phase current sense signal or a first duration has elapsed.