We report a method to prepare hydrophilic poly(dimethylsiloxane) (PDMS) stamps that could transfer patterns of polar molecules homogeneously in soft lithography. In this method, we demonstrated a two-step procedure by using a mixed gas of argon (Ar) and hydrogen (H-2)-based microwave plasma pretreatment to activate PDMS and subsequent acrylonitrile grafting onto PDMS, generating a hydrophilic surface with cyano (-CN) group coatings. The PDMS hydrophilic surface exhibited high affinity for wetting acetonitrile, which is a conventional solvent for DNA synthesis. Acetonitrile droplets possessed contact angles as low as 17 +/- 7degrees on the cyano (-CN) groups grafted PDMS stamps surface. The hydrophilicity was stable and could last for at least 1 month at room temperature. Attenuated total reflectance Fourier transform infrared spectroscopy and X-ray photoelectron spectrum were used to characterize the surface hydrophilization. Such a hydrophilic and inert PDMS stamp showed significance for reactive multilevel fabrications in soft lithography. The possible chemical mechanism for PDMS surface grafting was discussed.