Nanometer- scale proximal probe thermal desorption/electrospray ionization mass spectrometry (TD/ESI-MS) was demonstrated for molecular surface sampling of caffeine from a thin film using a 30 nm diameter nanothermal analysis (nano-TA) probe tip in an atomic force microscope (AFM) coupled via a vapor transfer line and ESI interface to a MS detection platform. Using a probe temperature of 350 °C and a spot sampling time of 30 s, conical desorption craters 250 nm in diameter and 100 nm deep were created as shown through subsequent topographical imaging of the surface within the same system. Automated sampling of a 5 × 2 array of spots, with 2 μm spacing between spots, and real time selective detection of the desorbed caffeine using tandem mass spectrometry was also demonstrated. Estimated from the crater volume (∼2 × 10(6) nm(3)), only about 10 amol (2 fg) of caffeine was liberated from each thermal desorption crater in the thin film. These results illustrate a relatively simple experimental setup and means to acquire in an automated fashion submicrometer scale spatial sampling resolution and mass spectral detection of materials amenable to TD. The ability to achieve MS-based chemical imaging with 250 nm scale spatial resolution with this system is anticipated.