The authors present a cyber-physical systems related study on the estimation and prediction of driver states in autonomous vehicles. The first part of this study extends on a previously developed general architecture for estimation and prediction of hybrid-state systems. The extended system utilizes the hybrid characteristics of decision-behavior coupling of many systems such as the driver and the vehicle; uses Kalman Filter estimates of observable parameters to track the instantaneous discrete state, and predicts the most likely outcome. Prediction of the likely driver state outcome depends on the higher level discrete model and the observed behavior of the continuous subsystem. Two approaches to estimate the discrete driver state from filtered continuous observations are presented: rule based estimation, and Hidden Markov Model (HMM) based estimation. Extensions to a prediction application is described through the use of Hierarchical Hidden Markov Models (HHMMs). The proposed method is suitable for scenarios that involve unknown decisions of other individuals, such as lane changes or intersection precedence/access. An HMM implementation for multiple tasks of a single vehicle at an intersection is presented along with preliminary results.