P>Although much is known about the structure and biosynthesis of microbial cell envelope constituents, the three-dimensional organization, assembly and interactions of the individual components remain poorly understood. How do cell walls remodel during cell growth or incubation with drugs? What is the supramolecular architecture of proteins in bacterial surface layers, in outer membranes and in intracytoplasmic membranes? What is the spatial arrangement of cell surface receptors, clustered or homogeneous? What are the adhesive and mechanical properties of cell surface proteins and how are they related to function? Traditionally, these questions have been difficult - or impossible - to address owing to the lack of high-resolution single-cell and single-molecule probing techniques. With its ability to observe and force probe the cell envelope down to the molecular level under physiological conditions, atomic force microscopy (AFM) has recently offered new opportunities in molecular microbiology. While high-resolution AFM imaging is a powerful tool for visualizing the architecture of cells and membranes in buffer solution, force spectroscopy offers a means to analyse the localization, interactions and elasticity of their individual constituents. These nanoscale experiments complement microscopy, genetics and biochemical methods traditionally used to analyse the microbial envelope.