System identification is a key step for model- based control, estimator design, and output prediction. This work considers the offline identification of partially observed nonlinear systems. We empirically show that the certainty-equivalent approximation to expectation-maximization can be a reliable and scalable approach for high-dimensional deterministic systems, which are common in robotics. We formulate certainty-equivalent expectation-maximization as block coordinate-ascent, and provide an efficient implementation. The algorithm is tested on a simulated system of coupled Lorenz attractors, demonstrating its ability to identify high-dimensional systems that can be intractable for particle-based approaches. Our approach is also used to identify the dynamics of an aerobatic helicopter. By augmenting the state with unobserved fluid states, a model is learned that predicts the acceleration of the helicopter better than state-of-the-art approaches.