A robotic instrument system having an elongate sheath instrument and an elongate catheter instrument positioned within a working lumen of the sheath instrument is controlled by selectively operating an instrument driver coupled to the catheter instrument to place a control element extending through the catheter instrument in tension, and thereby articulate at least a distal end portion the catheter instrument, while automatically compensating for a torsional force exerted on the sheath instrument in a first direction due to articulation of the distal end portion of the catheter, by urging the sheath instrument to twist in a second direction opposite of the first direction.