In molecular electronics, it is critical to minimize the sources that can result in defective electrodes, such as contaminations related to the fabrication process (photoresist and organic residues) or roughening of the electrode during etching, because these defects hamper the formation of well‐organized molecular structures. Junctions based on micropores are desirable as they are scalable, but micropores are not fabricated on ultrasmooth template‐stripped electrodes, and may suffer from stray capacitances and leakage currents across the insulating matrix. A method is reported to fabricate micropores in AlOx
on template‐stripped Au based on a two‐step etch process so that the Au surface is not in direct contact with photoresistance during the fabrication process. These junctions do not suffer from stray capacitances or leakage currents, enable temperature variable measurements down to 8.5 K, have excellent current retention characteristics, and are stable for at least 2 months. By analyzing the normalized differential conductance curves and detailed comparison against junctions with cone‐shaped tips of EGaIn and EGaIn stabilized in a through‐hole in polydimethylsiloxane, how the surface roughness of top electrodes affects the effective contact area, influences the symmetry of the response of the junctions, and how the electrical characteristics scale with molecular length are established.