Achieving precise state estimation is needed for the unmanned aerial vehicle to perform a successful flight with a high degree of stability. Nonetheless, obtaining accurate state estimation is considered challenging due to the inaccuracies associated with the measurements of the onboard commercial-offthe-shelf (COTS) Inertial Measurement Unit (IMU). The immense vibration of the vehicle's rotors makes these measurements suffer from issues like; large drifts, biases and immense unpredictable noise sequences. These issues cannot be significantly tackled using classical estimators and an accurate sensor fusion technique needs to be developed. In this paper, a deep learning framework is developed to enhance the performance of the state estimator. A deep neural network (DNN) is trained using a deep-learning-based technique to identify the associated measurement noise models and filter them out. Dropout technique is adopted for training the DNN to avoid overfitting and reduce the complexity of nets computations. Compared to the classical estimation results, the proposed deep learning technique demonstrates capabilities in identifying the measurement's noise characteristics. As an example, an enhancement in estimating the attitude states at near hover is proved using this approach. Furthermore, an actual hover flight was performed to validate the proposed estimation enhancement method.