Although extensive amounts of research have been carried out on superconductor-normal metal-superconductor (SNS) electronic devices, the fabrication of superconductor SNS devices still remains difficult. Surface modification of high-temperature superconductors could be a way to control the interface of SNS electronic device fabrication. Here, we developed a cleaning method for thin films of high-temperature superconductor surface based on self-assembled monolayers. High-quality c-axis orientated YBa2Cu3O7−δ (i.e., YBCO) and Y0.6Ca0.4Ba1.6La0.4Cu3O7−δ (i.e., TX-YBCO) thin films were deposited by standard laser ablation methods. YBCO/Au/YBCO and TX-YBCO/Au/TX-YBCO planar type junctions were fabricated by photolithography, focused-ion-beam milling, and ex situ sputter depositions. A 40–50 nm nanotrench was ion milled on the thin film by FIB, and a thin gold layer was deposited by an ex situ method on the nanotrench to connect the two separated high-temperature superconductor electrodes. SEM, AFM, and R vs T resistivity measurements were used to compare the corrosion layer formed in the interface of the SNS junctions with the SAM cleaned SNS junction. Evidence here suggests that the SAM cleaning method can be used to remove the degradation layer on the surface of cuprate superconductors. The obtained contact resistivity value, (10−8 Ω cm2) for a SNS junction with SAM treatment is comparable with that of SNS junctions fabricated by the in situ methods.