When designing a chemistry education research study it is important that the researcher select or create assessment instruments and methodologies that are valid. This ensures that correct interpretations can be made from the data collected using the instrument or methodology. The two studies described here introduce a novel method for investigating students' structural knowledge of chemistry topics using a program called Pathfinder. In these studies, the Pathfinder program is investigated for validity (content, construct, criterion, and concurrent), as well as its sensitivity to changes in students' structural knowledge. Once shown to be valid when used properly, the Pathfinder program can then be employed in future chemistry education research studies to investigate students' structural knowledge.