Organic molecules such as porphyrins and alkanethiols are currently being investigated for applications such as sensors, light-emitting diodes and single electron transistors. Porphyrins are stable, highly conjugated compounds and the choice of metal ion and substituents bound to the macrocycle as well as other effects such as chemical surrounding and cluster size modulate the electronic and photonic properties of the molecule. Porphyrins and their derivatives are relatively non-toxic and their very rich photo- and electro-chemistry, and small HOMO-LUMO gaps make them outstanding candidates for use in molecularly-enhanced electronic applications. For these studies, self-assembled tri-pyridyl porphyrin thiol derivatives have been fully characterized on Au(111) surfaces. A variety of surface characterization techniques such as Atomic Force Microscopy (AFM), Scanning Tunneling Microscopy (STM), FT-IR spectroscopy and X-ray photoelectron spectroscopy (XPS) have been implemented in order to obtain information regarding the attachment orientation based on the angle and physical height of the molecule, conductivity which is determined based on the apparent height and current-voltage (I-V) measurements of the molecule, conductance switching behavior due to conformational or other effects as well as the stability of the molecular ensembles. Specifically, the transport properties of free base and zinc coordinated tri-pyridyl porphyrin thiol molecular islands inserted into a dodecanethiol matrix on Au(111) were investigated using STM and cross-wire inelastic electron tunneling spectroscopy (IETS). The zinc porphyrin thiol islands observed by STM exhibited reversible bias induced switching at high surface coverage due to the formation of Coulomb islands of ca. 10 nm diameter driven by porphyrin aggregation. Low temperature measurements (~ 4 K) from crossed-wire junctions verified the appearance of a Coulomb staircase and blockade which was not observed for single molecules of this compound or for the analogous free base. Scanning probe lithography via nanografting has been implemented to directly assemble nanoscale patterns of zinc porphyrin thiols and 16-mercapotohexadecanoic acid on Au surfaces. Matrix effects during nanopatterning including solvent and background SAMs have been investigated and ultimately ~ 10 nm islands of zinc porphyrins have been fabricated which is the optimal size for the observed switching effect.