Abstract The current state of particle physics is conflicting. One has a marvellously working theory, the Standard Model, that leaves many questions open. This tension has led to a variegated landscape of models of physics beyond the Standard Model that is guided by epistemic and pragmatic values of model preference. Whereas these preferences are shared by experimentalists and theorists, their use of models within research practice differs. Experimentalists focus on event signatures that have many-to-many relations to models. We argue that physicists’ three-pronged approach distinguishing raw data, signatures, and models resembles the analysis of Bogen and Woodward, establishing the autonomy of phenomena. Using signatures opens the door for explorative experimentation, which becomes crucial for managing the uncertainty about the direction of particle physics that has emerged after the discovery of the Higgs boson.