A review of the educational literature on naive concepts about principles of chemistry and physics and surveys of science museum visitors reveal that people of all ages have robust alternative notions about the nature of atoms, matter, and bonding that persist despite formal science education experiences. Some confusion arises from the profound differences in the way that scientists and the lay public use terms such as materials, metals, liquids, models, function, matter, and bonding. Many models that eloquently articulate arrangements of atoms and molecules to informed scientists are not widely understood by lay people and may promote naive notions among the public. Shifts from one type of atomic model to another and changes in size scales are particularly confusing to learners. People's abilities to describe and understand the properties of materials are largely based on tangible experiences, and much of what students learn in school does not help them interpret their encounters with materials and phenomena in everyday life. Identification of these challenges will help educators better convey the principles of materials science and engineering to students, and will be particularly beneficial in the design of the Materials MicroWorld traveling museum exhibit.