Alkanethiolate self-assembled monolayers on Au{111} are used for the two-dimensional matrix isolation of conjugated organic thiolates, studied for their potential to act as molecular wires. The conjugated organic molecules are inserted from dilute solution into boundaries between structural domains and at substrate step edges of preassembled n-alkanethiolate monolayers so as to preserve the order of the initial alkanethiolate lattice. In contrast, when both molecules are codeposited from a single solution, the structure of the assembled monolayer shows no ordered molecular lattice of the alkanethiol component. Scanning tunneling microscopy measurements on the isolated conjugated component molecules show them to have enhanced conductivity compared to neighboring alkanethiolates.