One particular challenge in chemistry learning is developing students' atomic level understanding of chemical processes. It is necessary to help students learn how to critique atomic models rather than accept them as ''truth.'' In this study, we used a resources-based framework to examine how students made sense of macroscopic level information to account for what was happening at the atomic level. We interviewed 20 students enrolled in the first semester of general chemistry. Each student completed three exercises. The first exercise involved a card sorting task and the second exercise involved constructing an atomic model to learn how students made sense of the atomic level of a reaction involving the mixing of aqueous silver nitrate and aqueous sodium chloride to produce a precipitate. Next, students engaged in an exercise in which they were shown three conflicting atomic level animations of the same experiment and they were charged with selecting the animation that was most scientifically accurate. We analyzed the general patterns of characterization that emerged when students engaged in the card sorting and modeling exercise and the conflicting animation exercise using a resources framework. We contend that students apply and sometimes misapply knowledge resources to make sense of the atomic level. The process affects decisions that they make and stances that they develop about the accuracy of atomic level models.