Self-assembled monolayers (SAMs) of alkyl and fluorinated thiols were investigated after ozonolysis shadow mask treatments with varying areal domains and after exposure to displacing thiols. Imaging near edge X-ray absorption fine structure (NEXAFS) spectroscopy was used as a novel method for investigating the resulting heterogeneous SAM films. Composition and work function were characterized via X-ray and ultraviolet photoelectron spectroscopy, respectively. Imaging NEXAFS characterization of these heterogeneous films clearly shows the displacement of oxidized thiols after ozonolysis patterning. Changes in the SAM after patterning, and after displacement from back-filling thiols, can be inferred from changes in the effective work function. Larger changes in work function were observed for cases where thiols were deposited after ozonolysis suggesting that the displacing SAM was denser and/or more ordered than as-deposited films. These results highlight one of the first demonstrations of imaging NEXAFS and present measurements of effective work function on intentionally heterogeneous SAM films. Copyright © 2013 John Wiley & Sons, Ltd.