Large area self-assembled monolayers (SAMs) based tunneling junctions have recently received heightened attentions, in part, due to high yield of working junctions, ease of fabrication, and data reproducibility. Eutectic gallium indium (EGaIn) and ultra-flat metal substrate are used to form these molecular junctions. Despite the advances, effect of sub-nanometer roughness inhibits delineation of second-order effects on tunneling characteristics. These effects, like intra-molecular keesom interactions, can lead to new approaches to tuning charge transport behavior – a fete that is yet to be harnessed. To address this challenge, we deployed a three-pronged approach entailing; i) polishing of the top-electrode, ii) tuning roughness of the bottom electrode and the angstrom scale, and iii) deploying statistical analysis to uncover these effects. In this talk, effect of these modifications on SAM and associated charge transport behavior will be discussed.