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We report our studies of the nanolithographic surface modifications induced by an Atomic Force Microscope (AFM) in epitaxial thin films of oxygen deficient Lanthanum Barium Manganese Oxide (La0.67Ba0.33MnO3−δ). The pattern characteristics depend on the tip voltage, tip polarity, voltage duration, tip force, and humidity. We have used Electron Energy Dispersive X-Ray Spectroscopy (EDS) to analyze the chemical changes associated with the surface modifications produced with a negatively biased AFM tip. A significant increase in the oxygen stoichiometry for the patterned regions relative to the pristine film surface is observed. The results also indicate changes in the cation stoichiometry, specifically a decrease in the Lanthanum and Manganese concentrations and an increase in the Barium concentration in the patterned regions.