While in the recent studies we utilized microwave plasma energy to react imidazole molecules to cross-linked poly(dimethylsiloxane) (PDMS) surfaces, the issue of surface morphological changes resulting from microwave plasma reactions of imidazole on PDMS surfaces remained open. In this study, we will combine attenuated total reflectance Fourier transform infrared analysis and atomic force microscope measurement to establish inhibition mechanism of silica and morphological changes resulting from both closed and open flow reactor conditions. These studies show that silica containing PDMS is composed of PDMS-rich and silica-rich domains. The aggregations of silica particles in silica-rich domains is responsible for the inhibition of imidazole reactions on PDMS surfaces. Under a closed reactor condition, a multilayer of imidazole rings is formed on PDMS surfaces. On the other hand, in an open flow reactor condition, imidazole ring is opened and grafted to form -(CH=CH)(n)- species on PDMS surfaces.