This paper presents an online path planning algorithm for safe autonomous manipulation of a flexibly constrained object in an unknown environment. Methods for real time identification and characterization of perceived flexible constraints and global stiffness are presented. Used in tandem, these methods allow a robot to simultaneously explore, characterize, and manipulate an elastic system safely. Navigation without a-priori knowledge of the system is achieved using constraint exploration based on local force and position information. The perceived constraint stiffness is considered at multiple poses along an object's (system) trajectory. Using stiffness eigenvector information, global stiffness behavior is characterized and identified using an atlas of simple mechanical constraints, such as hinges and planar constraints. Validation of these algorithms is carried out by simulation and experimentally. The ability to recognize several common simple mechanical constraints (such as a flexible hinge) in real time, and to subsequently identify relevant screw parameters is demonstrated. These results suggest the feasibility of simultaneous global constrain/stiffness exploration and safe manipulation of flexibly constrained objects. We believe that this approach will eventually enable safe cooperative manipulation in applications such as organ retraction and manipulation during surgery