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Software Product Line (SPL) engineering is a paradigm shift towards modeling and developing software system families rather than individual systems. It focuses on the means of efficiently producing and maintaining multiple similar software products, exploiting what they have in common and managing what varies among them. This is analogous to what is practiced in the automotive industry, where the focus is on creating a single production line, out of which many customized but similar variations of a car model are produced. Feature models (FMs) are a fundamental formalism for specifying and reasoning about commonality and variability of SPLs. FMs are becoming increasingly complex, handled by several stakeholders or organizations, used to describe features at various levels of abstraction and related in a variety of ways. In different contexts and application domains, maintaining a single large FM is neither feasible nor desirable. Instead, multiple FMs are now used. In this thesis, we develop theoretical foundations and practical support for managing multiple FMs. We design and develop a set of composition and decomposition operators (aggregate, merge, slice) for supporting separation of concerns. The operators are formally defined, implemented with a fully automated algorithm and guarantee properties in terms of sets of configurations. We show how the composition and decomposition operators can be combined together or with other reasoning and editing operators to realize complex tasks. We propose a textual language, FAMILIAR (for FeAture Model scrIpt Language for manIpulation and Automatic Reasoning), which provides a practical solution for managing FMs on a large scale. An SPL practitioner can combine the different operators and manipulate a restricted set of concepts (FMs, features, configurations, etc.) using a concise notation and language facilities. FAMILIAR hides implementation details (e.g., solvers) and comes with a development environment. We report various applications of the operators and usages of FAMILIAR in different domains (medical imaging, video surveillance) and for different purposes (scientific workflow design, variability modeling from requirements to runtime, reverse engineering), showing the applicability of both the operators and the supporting language. Without the new capabilities brought by the operators and FAMILIAR, some analysis and reasoning operations would not be made possible in the different case studies. To conclude, we discuss different research perspectives in the medium term (regarding the operators, the language and validation elements) and in the long term (e.g., relationships between FMs and other models).