An obstruction detection system for a robotic catheter system including a robotic catheter manipulator assembly including one or more catheter manipulation bases and one or more sheath manipulation bases. Each manipulation base may be generally linearly movable on one or more tracks relative to the robotic catheter manipulator assembly. The obstruction detection system may include one or more obstruction detection sensors disposed on the track or on the manipulation bases to detect an obstruction along a path of motion of one or more manipulation bases. A software system may be provided for monitoring movement of the catheter and sheath manipulation bases, and/or a status of the obstruction detection sensors.