Understanding physical phenomena in education often requires a good three-dimensional (3D) imagination. Visualization software mainly uses either active 3D virtual simulations or static two-dimensional cross-sections for presenting real physical systems. We performed a comparative study of students' comprehension of both visualization approaches in the field of fundamental liquid crystal (LC) phases. We also developed a mechanical teaching tool-three boxes with wooden rods attached on vertical strings, in order to simulate the transitions between LC phases. We found that both the software and mechanical visualizations are efficient for representation of LC phases as well as training natural science competences.