A robotic surgical system with an input device has two operational modes by which both steerable and non-steerable elongate instruments can be effectively controlled, such as steerable catheters which can move in at least three orthogonal axes and non-steerable guidewires which can move via axial insertion/retraction or axial rotation. The robotic surgical system may include mapping schemes and haptic feedback to enhance the functionality, operation and ease of use of the input device when controlling non-steerable elongate instruments such as guidewires.