The search for authentic science research tools to evaluate student understanding in a hybrid learning environment with a large multimedia component has resulted in the use of concept maps as a representation of student's knowledge organization. One hundred and seventy third-semester introductory university-level engineering students represented their understanding related to the atom in a concept map. A qualitative analysis of the data presented a more informative and complete picture of students' understanding as compared with most prominent scoring techniques in the literature. The detailed analysis method is illustrated by means of some students' concept maps and the overall results of the entire student population are discussed. The most striking difference between common and more insightful maps is the inclusion of additional clusters describing models of the atom, beyond the clusters that just describe the elements of atoms (e.g. protons, electrons, etc.) and their characteristics.