Students have misconceptions of size and scale cognition as they confuse molecules and cells. The team deployed a virtual reality (VR) learning tool, namely Scale Worlds, for K-12 students to use at school. The present work aimed to examine the experience and perception of immersive technology, and logistical challenges of integrating Scale Worlds into a science class. Ten students and three teachers were included in this study with informed consent. Scale Worlds was introduced as part of a science class and then semi-structured interview was conducted. Students’ experience with VR technology included physiological discomfort, psychological nervousness and uncertainty of technology, personal abilities and unfamiliarity, and hardware latency. However, students perceived Scale Worlds to be a useful tool that helped them visualize entities of different sizes, and allowed them to work collaboratively. Teachers expressed desire for more exciting content in Scale Worlds and further usability enhancement, as well as need for additional material preparation time. The team planned to return to the same middle school for another round of in-field study after addressing some of the reported challenges.