Carboxylic acid terminated self-assembled monolayers (SAMs) deposited on epitaxial gold substrates were activated in situ using a water-soluble carbodiimide and N-hydroxysuccinimide reagents. The activated monolayer was subsequently derivatized employing a model water-insoluble organic reagent, namely, dodecylamine, using N,N'-dimethylformamide as the patterning solvent. The amidation reaction was confined to localized surface regions by performing the chemistry within the boundaries of capillaries formed between the activated SAM surface and a microfluidic networking (muFN) poly(dimethylsiloxane) mold placed upon the surface. The atomic force microscope (AFM) was employed to characterize muFN-derivatized surfaces; changes in the image contrast consistent with muFN pattern features are observed. Through this process, pattern feature boundaries with micrometer resolution are observed; the muFN pattern features are replicated with great fidelity. Lateral force microscopy was employed to identify changes in the surface's physical properties due to the random distribution of alkyl chains within the sample. The pulsed force mode of operation of the AFM has also been used to map changes in the adhesion properties resulting from differences in the chemical composition of muFN-derivatized surfaces. Changes in the maximum force of adhesion consistent with muFN pattern features are observed.