The COVID-19 pandemic caused an unprecedented interruption in formal education for students across the globe. As a result, universities and institutes of higher education have shifted to online learning platforms and adopted virtual teaching to deliver courses online. However, concerns rose that engineering student training in nanotechnology specialties would suffer disproportionately from the cancelation of laboratory activities due their procedural nature. In response, we have developed a 3D virtual scanning electron microscope (SEM) laboratory to meet the educational needs of our engineering students in the challenging times of the COVID-19. Creation of 3D lab representation in augmented reality aims to help our students to visualize and understand the SEM concepts and its working principles as well as its functional components. This 3D SEM lab model is made widely accessible to every student where students can download the free augmented reality app on their mobiles or tablet computers. The 3D virtual lesson contains introductory audio, animated video and voice memos for not only giving the students important SEM information but also directing them to the learning content they should pay attention to. The main advantage of our innovation is the interaction with the 3D SEM model, allowing the students perform various on-screen learning activities with better spatial comprehension of SEM and immersive learning with mixed augmented virtual reality mode. Series of gamified learning activities and quizzes are embedded in the online lesson to enhance students’ engagement while monitoring their e-learning progress and results. A research survey conducted revealed that 98% of our students strongly agreed that this virtual SEM lab lesson was effective in their remote lab learning. This innovation represents a significant step towards digitalizing content delivery of nanotechnology education by integrating mobile device app into boundless teaching and learning practice in engineering curriculum. Our innovation was recently awarded 1st Runner Up in the IChemE EduSIG Innovative and Interactive Educational Game/Tool/App for Digital Classroom Competition.