HistoGuide application is a smartphone application system used by sixth form students as virtual microscopy and slides to solve the problems of incorrect drawing and labelling, inability to apply magnification and scale, and inability to observe details in microscopic practical works. However, as a newly developed application, there are still many who do not understand the usability of the HistoGuide application. In building a good application, one important part is good usability. Usability testing, especially in the HistoGuide application, can show users' ease and efficiency in using the system. The authors try to use qualitative usability testing through observation, document analysis and interviews with four participants as a pilot study before a real study. The analysis revealed the preference of the students for utilizing virtual microscopy as an educational tool in terms of usability, in the construct of usefulness, ease of use, ease of learning, satisfaction, effectiveness and efficiency. These results indicate that the HistoGuide application is good. The results of usability measurement are expected to help the development and improvement of the HistoGuide application in the future, besides gauging the students’ learning experience. The study also revealed that students accepted virtual microscopic learning tool that was easy to use, available at a distance, encouraged collaboration and mastery, changed learning attitudes and emulated the same concepts of optical microscopy. Although there are some concerns and challenges, the overall learning experiences are highly positive towards complementing optical microscopy with virtual microscopy.