Experiments are described that involve undergraduates learning concepts of nanoscience and chemistry. Students prepare nanopatterns of organosilane films using protocols of particle lithography. A few basic techniques are needed to prepare samples, such as centrifuging, mixing, heating, and drying. Students obtain hands-on skills with nanoscale imaging using an atomic force microscope (AFM) when they learn to characterize samples. Designed surfaces are made using a surface mask of latex or silica spheres to generate nanopatterns of organosilanes. An organic thin film is applied to the substrate using steps of either heated vapor deposition or immersion in solution. The steps for preparing samples are not complicated; however, the nanostructures that are produced by particle lithography are exquisitely regular in geometry and surface arrangement. At the molecular level, two types of sample morphology can be made depending on the step for depositing organosilanes. Ring-shaped nanostructures are produced with heated vapor deposition through a particle mask, and nanoholes are produced within a matrix film using immersion of masked substrates. Experience with advanced AFM instrumentation is obtained for data acquisition, digital image processing, and analysis. Skills with chemical analysis are gained with bench methods of sample preparation. Concepts such as the organization of molecules on surfaces and molecular self-assembly are demonstrated with the visualization of nanopatterns prepared by students. Experiments with particle lithography can be used as a laboratory module or for undergraduate research projects, and are suitable for students with a multidisciplinary science background.