Tailoring solid surfaces attracts a number of technological and scientific interest with numerous applications. One method to modify a solid surface is via the formation of a molecular film. The adsorbed molecules assemble spontaneously (self assemble) forming a monolayer that is called self-assembled monolayer (SAM). When dissimilar molecules are employed to form a SAM on a surface, separation into domains takes place, but the domain shapes that have been reported vary from irregular patches with highly non-uniform size distributions to disordered stripes or worm-like domains. It was postulated that the various morphologies observed to date were due to kinetic trapping. The scope of this thesis was to investigate the thermodynamic equilibrium for such monolayers. High quality one- and two-component thiol SAMs on flat Au(111) was produced and studied. The thiols that were used were Octanethiol (OT), 4-Cyano-1-butanethiol (CN4T), para-nitrothiophenol (NB4M) and 3-mercaptopropionic acid (MPA). The SAMs were produced via solution immersion. XPS and contact angle measurements verified the SAM formation. Cyclic voltammetry has been employed for the reductive desorption of the bounded thiols. The reductive potentials of the thiols have been measured at -0.97 V for OT, -0.79 V for CN4T, -0.75 V for the NB4M and -0.78 V for the MPA. The difference in the peak potentials facilitates our studying of binary SAMs by this method. Binary SAMs of OT:CN4T, OT:NB4M and OT:MPA at different feed ratios was produced via solution immersion. The surface composition of the OT:CN4T and OT:NB4M binary SAMs was determined by XPS. The CV analysis of the binary SAMs showed two distinct separated peaks at the reductive potentials of the two constituting thiols, which indicates the existence of phase separated macro domains onto the Au(111) surface. A large series of one- and two-component SAMs were thermally treated inside neat solvent at 60°C (annealing) for various amounts of time. XPS and contact angle measurements verified that the annealing process did not cause any alterations on the composition or the quality of the SAMs. Upon annealing, the evolution of the binary SAM surfaces was found to lead to new nanoscale thermodynamic phases as indicated by the voltammograms. The two-peak profiles that were seen at the non-annealed binary SAMs changed to three-peak profiles, with the appearance of a new peak at an intermediate potential. As the annealing time increased a single peak profile was received. The one-peak CV profiles remained unaltered (one peak at an intermediate potential) upon further annealing. The new phase is therefore the thermodynamically equilibrium phase. The new equilibrium phase was identified by STM. The new phases were found to depend on the choice of ligand and the composition. STM imaging elucidated further that the new phase can morphologically be stripes with an average width of ~3 nm for annealed SAMs of OT:CN4T and OT:NB4M, prestripes for OT:NB4M binary SAMs with higher OT concentration, while OT:CN4T at 20 days of annealing and OT:MPA 10:90 led to micellar domains in the size range from 4 to 8 nm as the thermodynamic phase. The work presented in this thesis has shown how the process of annealing leads to new thermodynamically equilibrium phases in binary SAMs. Due to this process, nanostructured surfaces with a variety of domains can be achieved in binary SAMs of thiols on flat Au(111) surfaces.