This paper introduces a framework for screening cargo containers for nuclear material at security stations throughout the United States using knapsack problem, reliability, and Bayesian probability models. The approach investigates how to define a system alarm given a set of screening devices, and hence, designs and analyzes next‐generation security system architectures. Containers that yield a system alarm undergo secondary screening, where more effective and intrusive screening devices are used to further examine containers for nuclear and radiological material. It is assumed that there is a budget for performing secondary screening on containers that yield a system alarm. This paper explores the relationships and tradeoffs between prescreening, secondary screening costs, and the efficacy of radiation detectors. The key contribution of this analysis is that it provides a risk‐based framework for determining how to define a system alarm for screening cargo containers given limited screening resources. The analysis suggests that highly accurate prescreening is the most important factor for effective screening, particularly when screening tests are highly dependent, and that moderately accurate prescreening may not be an improvement over treating all cargo containers the same. Moreover, it suggests that screening tests with high true alarm rates may mitigate some of the risk associated with low prescreening intelligence.