Traditional minimally invasive robots provide to the surgeon an interface for controlling the tip of the endoscopic arm in Cartesian space. We proposed therefore a similar interface for the STIFF-FLOP robot. The direct control of the tip pose was provided by an inverse kinematics component, computing the appropriate STIFF-FLOP robot configuration. Due to the flexibility of the arm modules, we have organized the inverse kinematics into two layers. The first one handles the inverse kinematics in a generic way. It is based on a numerical estimation of the robot. This layer is generic in the sense that it can incorporate any module representation, as long as the module representation provides a forward kinematics mechanism. The second layer concerns the kinematic modeling of the flexible modules, and has to provide forward kinematics functionalities for the upper model. Instead of the standard constant curvature parameters, we are proposing two other representations, one using each module tip position, and the other one directly using the chamber lengths. The flexible modules are connected to a robotic arm through a rigid rod, to extend the operational space of the system. The robotic arm pose is encoded with an adaptation of the spherical coordinate system to ensure that the rod entering the human body respects the single insertion point constraint. By defining a forward kinematics for the rod pose, the external robot end effector is implicitly embedded into the general inverse kinematics scheme, so that the estimation of the flexible modules’ configurations and the pose of the robot end-effector are all computed together to follow the motion requests provided by the surgeon..