The operational characteristics and imaging performance are described for a new instrument comprising an atomic force microscope coupled with a pulsed laser and a linear ion trap mass spectrometer. The operating mode of the atomic force microscope is used to produce topographic surface images having sub-micrometer spatial and height resolution. Spatially resolved mass spectra of ions, produced from the same surface via microprobe-mode laser desorption/ionization at atmospheric pressure, are also used to create a 100 x 100 microm chemical image. The effective spatial resolution of the image (approximately 2 microm) was constrained by the limit of detection (estimated to be 10(9)-10(10) molecules) rather than by the diameter of the focused laser spot or the step size of the sample stage. The instrument has the potential to be particularly useful for surface analysis scenarios in which chemical analysis of targeted topographic features is desired; consequently, it should have extensive application in a number of scientific areas. Because the number density of desorbed neutral species in laser desorption/ionization is known to be orders-of-magnitude greater than that of ions, it is expected that improvements in imaging performance can be realized by implementation of post-ionization methods.