Rapid increase of UAV operation in the next decade in areas of on-demand delivery, medical transportation services, law enforcement, traffic surveillance and several others pose potential risks to the low altitude airspace above densely populated areas. Safety assessment of airspace demands the need for a novel UAV traffic management (UTM) framework for regulation and tracking of the vehicles. Particularly for low-altitude UAV operations, quality of GPS measurements feeding into the UAV is often compromised by loss of communication link caused by presence of trees or tall buildings in proximity to the UAV flight path. Inaccurate GPS locations may yield to unreliable monitoring and inaccurate prognosis of remaining battery life and other safety metrics which rely on future expected trajectory of the UAV. This work therefore proposes a generalized monitoring and prediction methodology for autonomous UAVs using in-time GPS measurements. Firstly, a typical 4D smooth trajectory generation technique from a series of waypoint locations with associated expected times-of-arrival based on B-spline curves is presented. Initial uncertainty in the vehicle's expected cruise velocity is quantified to compute confidence intervals along the entire flight trajectory using error interval propagation approach. Further, the generated planned trajectory is considered as the prior knowledge which is updated during its flight with incoming GPS measurements in order to estimate its current location and corresponding kinematic profiles. Estimation of position is denoted in dicrete state-space representation such that position at a future time step is derived from position and velocity at current time step and expected velocity at the future time step. A linear Bayesian filtering algorithm is employed to efficiently refine position estimation from noisy GPS measurements and update the confidence intervals. Further, a dynamic re-planning strategy is implemented to incorporate unexpected detour or delay scenarios. Finally, critical challenges related to uncertainty quantification in trajectory prognosis for autonomous vehicles are identified, and potential solutions are discussed at the end of the paper. The entire monitoring framework is demonstrated on real UAV flight experiments conducted at the NASA Langley Research Center.