The problem of aircraft conflict detection and resolution (CDR) in uncertainty is addressed in this thesis. The main goal in CDR is to provide safety for the aircraft while minimizing their fuel consumption and flight delays. In reality, a high degree of uncertainty can exist in certain aircraft-aircraft encounters especially in cases where aircraft do not have the capabilities to communicate with each other. Through the use of a probabilistic approach and a multiple model (MM) trajectory information processing framework, this uncertainty can be effectively handled. For conflict detection, a randomized Monte Carlo (MC) algorithm is used to accurately detect conflicts, and, if a conflict is detected, a conflict resolution algorithm is run that utilizes a sequential list Viterbi algorithm. This thesis presents the MM CDR method and a comprehensive MC simulation and performance evaluation study that demonstrates its capabilities and efficiency.