Microwave plasma reactions of imidazole, 2-methylimidazole, and 2-ethylimidazole on poly(dimethylsiloxane) (PDMS) surfaces resulted in the formation of species containing conjugated surface domains which can be utilized for further reactions. When imidazole and its derivatives were used, polymerization of imidazole and the formation of C=C and CN conjugated species occurred. However, the extent of reactions for each monomer depends on not only the reaction time but also the molecular structure. For methyl- and ethyl-substituted imidazole, more stable radical species are generated and sustain their excited state in the high-energy plasma environments. Specifically, dehydrogenated 2-methyl, 2-ethylimidazole radicals and (*)N=CR-NH(*) (R = -CH(3), -CH(2)CH(3)) species exhibit higher stability than dehydrogenated imidazole radicals and (*)N=CH-NH(*) species under plasma reaction conditions. Such prepared surfaces are capable of attaching antimicrobial drugs via the Pinner synthesis. These studies show that it is possible to react antimicrobial species such as chloramphenicol, and this promising approach offers numerous applications of microwave plasma reactions in biotechnology. Quantitative analysis of the depth of surface reactions was accomplished by using variable angle ATR FT-IR spectroscopy.