The combination of high speed photogrammetry, geometrically exact finite element models, and extended Kalman filters provides a very general tool capable of reconstructing the motion of complicated structures. This work presents the formulation, implementation, and demonstration of this tool on test structures. High-speed photogrammetry of complicated systems presents a useful method to measure the dynamics of a system without contacting it. This can be advantageous when it would be difficult or too time-consuming to alter or modify a system my mounting sensors. Additionally if the structure is very light, such as in biological systems like flying insects, mounting sensors is not an option. Issues arise since the use of correlated image data is incomplete and noisy. The entire surface of a body’s motion may not be visible throughout a dynamic event, thus introducing more uncertainty. To mitigate this, as well as provide an estimate of the error, an extended Kalman filter is used to approximate the states of a geometrically exact finite element model. Though computationally expensive, this filter is well-studied and robust. The finite elements are discretized in time using the Generalized alpha method, which is a member of the well-known Newmark family of time stepping methods. Previous efforts include the use of shadow castings to build the maximal volume in which the deformed body must be inside. The minimization of an energy function then provided a solution for the state of the body for a specific instance in time. This method does not provide an estimate of the uncertainty, and that motivates the use of the extended Kalman Filter. This filter also permits the generalization to uncertainty in the parameters of the structure as well. This work presents tests on several mechanically excited structures. It is the first step towards building the apparatus to study free-flying insects. Using multiple, synchronized cameras to capture free flying insects permits natural untethered flight and behaviors to be captured, reconstructed, and analyzed. The ability to accurately reconstruct the motion of free flying insects presents a treasure trove of data. Using this information as inputs to numerical fluid-structure simulations would permit modeling and load estimation.