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While photopatterning is in widespread use for patterning inorganic semiconductors, patterning of widely-used gold-thiol organic self-assembled monolayers is typically done with contact methods. Through common atomic force microscope techniques and quantification of the energy impinging on the target surface, the energy required for UV-photooxidation of Au-Thiol SAMs can be determined. This quantification allows for the precise control of features using simple shadow masking from electron microscopy grids or other targets. Beyond characterizing the accuracy and resolution of features, the pattern stability of the resulting monolayers is examined indicating a drive toward phase segregation and increasing order of the mixed monolayers.