The atomic force microscope (AFM) has emerged as an important complementary apparatus in the molecular biologist’s toolkit. At its core, AFM consists of a nanoscale force probe interacting with a sample. AFM is inherently a single-molecule technique. In contrast, bulk techniques yield ensemble averages, which can mask a range of unique, asynchronous activities. In addition to imaging, AFM can be used in force spectroscopy mode to unfold proteins mechanically. This provides a detailed view of the energy landscape that stabilizes macromolecular structure. Our laboratory has developed precision AFM apparatus designed for imaging and force spectroscopy of membrane proteins and lipophilic peptides in near-native conditions. In one project we shed light on core components of the general secretory system of E. coli. We observed the dynamic structure of the integral membrane translocon SecYEG in a lipid bilayer as well as its interactions with the peripheral ATPase SecA and precursor proteins. In another project we affixed lipophilic peptides to the AFM tip and directly observed the mechanical consequences of partitioning into the bilayer at the single amino acid level. Together with analytical modeling and molecular dynamics simulations, the results represent a step towards understanding the forces and kinetic pathways driving protein-bilayer partitioning. In this talk I will discuss these two projects and highlight a few of the novel aspects of our precision instrumentation along the way.