Amorphous carbon thin films are easily deposited at room temperature, readily functionalized with alkene-containing molecules through a UV photochemical reaction, and provide a robust surface capable of supporting array fabrication. Relatively few attachment chemistries for the fabrication of small organic molecule and/or biomolecule arrays on carbon substrates have been described to date. Here, acyl chloride-terminated amorphous carbon substrates were fabricated, characterized, and used to attach alcohol-, thiol-, and amine-containing small molecules. Oligonucleotide arrays of thiol- and amine-modified oligonucleotides were also prepared on these substrates. The hybridization density, average fluorescence signal of hybridized features, and average background fluorescence of oligonucleotide arrays prepared on acyl chloride-modified substrates were compared to the same parameters for oligonucleotide arrays prepared on maleimide- and aldehyde-modified substrates.