Nano-scale organic dielectric layers for organic thin film transistor (OTFT) were synthesized by the molecular-ruler method. Molecular-ruler method has been known as a good process to fabricate nano-scale structures for nano-devices with the advantages of low cost and high throughput. In this work, 16-mercaptohexadecanoic acid (16-MHDA) was used to make compact layers on gold substrate by self-assembled monolayer (SAM) and copper (II) was also used as a linker ion between 16-mercaptohexadecanoic acid (16-MHDA) layers. Finally multiple layer-by-layer structures of 16-mercaptohexadecanoic acid (16-MHDA) and copper (II) were fabricated. X-ray fluorescence (XRF) spectroscopy, x-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), infrared (IR) spectroscopy and scanning electron microscope (SEM) methods were utilized to verify the character of these structures.