This paper develops the first parts of a logical framework for the empirical sciences, by means of a redefinition of theory structuralism as originally developed by Joseph Sneed, Wolfgang Stegmüller, and others, in the context of a ‘rigid’ logic as based on a fixed (therefore rigid) ontology. The paper defends a formal conception of the empirical sciences that has an irreducible ontological basis and is unable, in general, to provide purely structural characterizations of the domain of a theory. The extreme rationalist utopia of a characterization of the real world ‘up to isomorphism’, therefore, is rejected.