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The research presented in this dissertation is focused on the construction of complex molecular structures on planar gold and silicon dioxide surfaces using a variety of surface modification techniques, along with thorough surface characterization at each modification step. The dissertation is structured into six separate chapters. In Chapter 1, an introduction to the importance and implications of molecular level surface modification, commonly employed surface modification methods, and available surface characterization techniques is presented. Chapter 2 shows applications of novel methodologies for the functionalization of gold surfaces using alkane dithiol self-assembled monolayers and thiol-ene click chemistry. The resulting functionalized gold substrates demonstrate higher chemical stability than alkanethiol self-assembled monolayers alone and allow spatially controlled functionalization of gold surfaces with light. In Chapter 3, work on tunable hydrophobic surfaces is presented. These surfaces are prepared using a combination of organosilane chemistry, layer-by-layer polyelectrolyte deposition, and thiol-ene chemistry. These hydrophobic surfaces demonstrate high mechanical and chemical stability, even at low pH (1.68). The pinning of water droplets could be tuned on them by the extent of their thermal treatment. Comprehensive surface characterization using X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), spectroscopic ellipsometry, atomic force microscopy, and water contact angles was carried out on the molecular assemblies prepared on gold and silicon dioxide surfaces. Chapters 4 and 5 are focused on the application, data interpretation, and enhancement in sensitivity of different surface characterization methods. In Chapter 4, XPS, ToF-SIMS, and principal components analysis are used to probe a real world corrosion-type problem. This systemic study showed the destruction of a protective coating composed of a nitrilotris(methylene)triphosphonic acid by a low-intensity fluorine plasma. In Chapter 5, enhancement in ToF-SIMS signals is shown via bismuth metal deposition. These surfaces are also probed by spectroscopic ellipsometry using the interference enhancement method. Finally, Chapter 6 concludes this dissertation by describing possible future work.