In this paper, we present a multi-dimensional study concerning Heisenberg's "gamma ray microscope", a thought experiment, which is intimately connected with the historical development of quantum mechanics (QM), and also with the most disputed interpretations of quantum theory. In this study: (a) we investigate how philosophers of science read and explicate the function of thought experimentation in physical science; (b) in the light of relevant philosophical theories, we examine the complicated epistemological questions raised by the "gamma-ray microscope" during the birth-process of QM and the contribution of this thought experiment to the clarification of the physical meaning of Heisenberg's indeterminacy relations; (c) on the basis of the preceding analysis, we propose an instructional intervention, which aims at leading learners not only to an essential understanding of QM worldview, but to a deep insight into the Nature of Science as well.