Models are one of the critical instruments of modern science. We know that models function in a variety of different ways within the sciences to help us to learn not only about theories but also about the world. So far, however, there seems to be no systematic account of how they operate in both of these domains. The semantic view as discussed in the previous chapter does provide some analysis of the relationship between models and theories and the importance of models in scientific practice; but, we feel there is much more to be said concerning the dynamics involved in model construction, function and use. One of the points we want to stress is that when one looks at examples of the different ways that models function, we see that they occupy an autonomous role in scientific work. In this chapter we want to outline, using examples from both the chapters in this volume and elsewhere, an account of models as autonomous agents, and to show how they function as instruments of investigation. We believe there is a significant connection between the autonomy of models and their ability to function as instruments. It is precisely because models are partially independent of both theories and the world that they have this autonomous component and so can be used as instruments of exploration in both domains.