Patterned self-assembled monolayers (SAMs) of alkanethiolates (AT) on Au and Ag substrates were imaged and characterized by scanning photoelectron microscopy (SPEM). The patterns were prepared in situ by direct writing with the zone-plate-focused X-ray beam provided by the SPEM station. Whereas both AT/Au and AT/Ag behaved alike upon the irradiation, which resulted in similar contrasts in the fabricated patterns and similar microspot spectra from the irradiated areas, the intensity relationship between the patterned and nonpatterned areas changed by different pathways for the Au and Ag substrates after the exposure of the patterns to ambient. The SPEM data imply that weakly bound molecular fragments are desorbed from the irradiated areas upon air exposure in the case of Ag, whereas adsorption of airborne molecules from ambient occurs for the Au substrate. The origin of the observed differences is presumably related to the specific branching patterns of irradiation-induced modification of AT/Au and AT/Ag.