A newly designed atomic force microscope (referred to as “cross-sectional AFM” or “xAFM”) is demonstrated that enables tip–sample interactions to be studied directly from a cross-sectional scanning electron microscope (SEM) view during AFM operation. Previously, such interactions have only been modeled using computer simulations or sensor-generating data. The xAFM will allow researchers to acquire additional visual information not available with conventional microscopic techniques. The xAFM is operated in a tungsten filament SEM, by examining a grating sample that is cleaved and mounted on the sample scanner so that the cleaved cross section faces upwards toward the bottom of the electron column. The tip scans horizontally, parallel to and at a height slightly lower than the cross-sectional surface of the sample but within the depth of focus of the SEM. Three experiments are described that show the unique features of the xAFM. The first demonstrates direct observation of the “tip-convolution” in real-time SEM images. The second shows unambiguous identification of an artifact in the lateral force microscope, from which a “double dip” appears in the signal from a damaged tip in a backward scan of the grating surface. The third enables measurements from blurred SEM images of large-amplitude oscillating high-Q AFM cantilevers in vacuum.