Control and repair of defects at metal/molecule interfaces is central for the realization of molecular electronic circuits with reproducible performance. The fundamental mechanism governing defect (pore) evolution on mica supported metal surfaces, its propagation in self assembled molecular layers and its implications for molecular junction devices are discussed. Pore eradication by replacing mica with halide platforms coupled with elevated substrate temperature during metal deposition yields exceptionally ultraflat metal landscapes. In-situ scanning tunneling microscopy further substantiates molecular locking at defect sites and upon defect healing; the emergence of a closely packed 2-D molecular architecture is demonstrated with nanometer scale spatial resolution in liquids.