The scanning electron microscope (SEM) has evolved to become an indispensable tool for research and education in engineering, physics, nanotechnology, geosciences, materials science, biological sciences and other fields. However, training on a physical SEM is costly, time consuming, and often unavailable in economically disadvantaged areas. Advances in computer technology have made interactive three-dimensional (3D) virtual laboratory an effective tool for training in medicine and many engineering and technology fields. In the current work, in order to provide cost-effective hands-on training, a virtual 3D SEM was developed using the game development engine Unity 3D. It contains realistic 3D models of the physical components, created using 3ds Max ® , a software for 3D modeling and rendering. The components are manipulated with scripts programmed using C# and JavaScript and then paired with the corresponding model. Users may view and operate the virtual instrument, save images for further analysis, and write a report. The developed virtual SEM was tested on diverse groups of users at multiple institutions, each divided to treatment and control groups. Feedback from these tests was collected and used for improvements in the overall quality of the simulated experience. In addition, users reported the experience of training on the virtual SEM as enjoyable.