Trade studies have become an indispensable engineering activity and are often used in the early stages of system architecture development. A trade study evaluates alternatives based on criteria and systematic analysis to select the most balanced alternative to attain the desired objectives. In the cyber-physical systems or system of systems (SoS) design, a trade study is often a highly complex, time-consuming, and expensive activity requiring extensive resources and broad knowledge. In the dissertation the architecture descriptive frameworks, trade study processes and architecture evaluation methods are reviewed, by focusing on their application for trade study with the ability to automate the evaluation of SoS architectures. Furthermore, dissertation introduces and presents the UT3SA method, which provides the required process, guidelines, evaluation algorithms, and measurements to increase the quality of a trade study by reducing errors in evaluating alternative SoS architectures.