Understanding ongoing chemical processes in the laboratory requires constant shifting between different representational levels--the macroscopic, submicroscopic, and symbolic levels--and analysis of the various mechanistic features of each of these levels. Thus, the ability to explain observations of chemical phenomena with regard to their submicroscopic levels in the laboratory is a key requirement. Research shows that students have difficulty in discerning and comprehending the meaning and visualization of the submicroscopic level. Traditional laboratory instruction often fails to help students discern the relationship between their observations and the corresponding chemical processes. Consequently, there is a high demand for new teaching strategies which address these issues. Therefore, we developed and implemented a scaffold for the organic laboratory and tested it in a research study using qualitative methods. The scaffold encourages students to purposefully separate and connect the macroscopic and submicroscopic representational levels. The implementation of the scaffold was accompanied by semi-structured pre- and post-interviews with students (N = 22) and an analysis of students' work with the scaffold in the laboratory. We analysed students' sense-making approach while reflecting on organic syntheses before and after working with the scaffold, and characterized changes in their approach. The findings emphasize the need to develop further resources to support students' understanding of the submicroscopic level. Implications of these findings for research and teaching to foster meaningful learning in the organic laboratory are discussed.