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Jump Markov Linear Systems are convenient models for systems that exhibit both continuous dynamics and discrete mode changes. Estimating the hybrid discrete-continuous state of these systems is important for control and fault detection. Existing solutions for hybrid estimation approximate the belief state by maintaining a subset of the possible discrete mode sequences. This approximation can cause the estimator to lose track of the true mode sequence when the effects of discrete mode changes are subtle. In this paper, we present a method for active hybrid estimation, where control inputs can be designed to discriminate between possible mode sequences. By probing the system for the purposes of estimation, such a sequence of control inputs can greatly reduce the probability of losing the true mode sequence compared to a nominal control sequence. Furthermore, by using a constrained finite horizon optimization formulation, we are able to guarantee that a given control task is achieved, while optimally detecting the hybrid state. In order to achieve this, we present three main contributions. First, we develop a method by which a sequence of control inputs is designed in order to discriminate optimally between a finite number of linear dynamic system models. These control inputs minimize a novel, tractable upper bound on the probability of model selection error. Second, we extend this approach to develop an active estimation method for Jump Markov Linear Systems by relating the probability of model selection error to the probability of losing the true mode sequence. Finally, we make this method tractable using a principled pruning technique. Simulation results show that the new method applied to an aircraft fault detection problem significantly decreases the probability of a hybrid estimator losing the true mode sequence.