This paper reports a simple microwave plasma patterning of poly(dimethylsiloxane) (PDMS) surfaces, which is accomplished by allowing selective surface areas to microwave plasma exposure in the presence of gaseous monomer. When maleic anhydride is used for microwave plasma reaction in the presence of physical barrier on the PDMS substrate, the resulting patterned surfaces with chemically bonded maleic anhydride and carboxylic acid groups are generated. In this particular study we attached amoxicillin via ammonolysis under weak base conditions in the presence of a catalyst as well as poly( ethyleneglycol) (PEG). A combination of internal reflection IR imaging (IRIRI) and atomic force microscopy (AFM) revealed that amoxicillin and PEG can be readily reacted on the microwave plasma patterned PDMS surfaces. Surface areas directly exposed to microwave plasmons exhibit the highest reactivity due to higher content of functional groups. These studies also show that molecular weight of PEG has also significant effect on kinetics of surface reactions.