Images of integrated circuit cross sections may be acquired with the atomic force microscope (AFM) by introducing material-dependent topography through a series of selective etches. AFM images of a fully processed complementary metal-oxide-semiconductor inverter structure show excellent qualitative agreement with high resolution scanning electron microscope (SEM) images. Measurements of layer thicknesses and lateral dimensions, however, do not precisely correlate. These discrepancies are attributed to tip-sample convolution due to the finite cone angle and rounding of the probe. We describe a one-dimensional computer simulator that models the nonlinear geometrical interaction between a tip and sample. Simulation results are used to determine the tip shape from an AFM image of a feature of known dimensions. The tip influence can be subsequently deconvolved from a cross section AFM image, generating a more faithful reflection of the surface topography. We demonstrate that this scheme yields measurements that correlate well with those made by the SEM and suggest that AFM imaging may be a viable alternative for the inspection and metrology of IC cross sections.