Prior research on conceptual change has identified multiple kinds of misconceptions at different levels of representational complexity including false beliefs, flawed mental models, and incorrect ontological categories. We hypothesized that conceptual change of a mental model requires change in the "system of relations" between the features of the prior model. To test this hypothesis, we compared instruction aimed at revising knowledge at the mental model level called "holistic confrontation"--in which the learner compares and contrasts a diagram of his or her flawed mental model to an expert model--to instruction aimed at revising knowledge at the false belief level--in which the learner is prompted to self-explain the expert model alone. We found evidence that participants who engaged in holistic confrontation were more likely to acquire a correct mental model, and a deeper understanding of the systems of relations in the model than those who were prompted to self-explain the expert model. The results are discussed in terms of their implications for science instruction. (Contains 4 figures and 1 table.)