Soft X-ray scanning photoelectron microscopy (SPEM) was applied to image and characterize molecular patterns produced by electron irradiation of various aliphatic and aromatic thiol-derived self-assembled monolayers (SAMs). The observed chemical contrasts allowed us to monitor complex phenomena which occurred as a result of electron-beam patterning, the exposure of the patterned films to ambient, and the irradiation of the films by the X-ray microprobe during image acquisition. The latter effect has been analyzed in detail and utilized for direct lithographic writing in the SAM resists by the zone-plate-focused X-ray beam. The results demonstrate the capabilities of the SPEM technique both for chemical imaging and as a fabrication tool for micro- and nanolithography.