Patterning and fabrication of nanostructures on surfaces is a great demand for nanoscale electronic and mechanical devices. Current techniques such as electron beam lithography and photolithography provides limited resolution and they are not capable of reproducible in nanoscale. Among those, Scanning Probe Microscopy (SPM) lithography that uses a nanometer sharpened tip has demonstrated outstanding capabilities for nanometer level patterning on various surfaces. Moreover, SPM techniques offer creating nanopatterns of Self Assembled Monolayers (SAMs) with molecular precision and visualizing surfaces with the highest spatial resolution. In this work, nanoscratches on gold surfaces and oxidation patterns on titanium surface were successfully performed as example of SPM lithography. In the second stage, Octadecylamine-HCl, Octadecanetiol (ODT) and Decylmercaptan (DM) SAM organic films were fabricated on various substrates; i.e., mica, silica, titanium surface deposited on silicon, n and p type silicon, using self assembly film preparation techniques. The film thicknesses were measured with Atomic Force Microscope (AFM). Nanopatterns were fabricated on SAM films using AFM tip by exerting a local high pressure at the contact that causes the displacement of SAM molecules by a high shear force. It was observed that there was no formation of SAMs on n type Si and silica substrates whereas there were organic assemblies on the other substrates. Fabricated nanopatterns were examined and thickness measurement was done. Molecular lengths of the organics were evaluated by using of SPARTAM 02 LINUX-UNIX with the method of PM3 and the measured values were compared with the calculated ones and it was concluded that monolayers were formed on the surfaces.