Site-specific masking with graphene films has the potential to facilitate low-cost, high-throughput micro-patterns on silicon substrates over large areas. Here, a facile approach to using graphene as a masking agent on silicon wafers for site-specific patterning is demonstrated. Graphene sheets were deposited via a sealing-tape-exfoliation method onto hydride-terminated (Si-H) silicon substrates. Raman confocal mapping showed inhibition of oxidation of the Si wafer underlying the graphene, indicating that the graphene restricts the diffusion of oxygen onto the Si surface. The graphene coated Si substrates were then electrochemically etched in an aqueous HF/ethanol (3:1 (v/v)) anodization solution. Scanning electron microscopy showed that the graphene layer successfully restricted the etching of the Si surface, however, near the edge sites of the graphene deep etching occurred.