Two-dimensional (2D) atomic crystals and their hybrid structures have recently attracted much attention due to their potential applications. The fabrication of metallic contacts or nanostructures on 2D materials is very common and generally achieved by performing electron-beam (e-beam) lithography. However, e-beam lithography is not applicable in certain situations, e.g., cases in which the e-beam resist does not adhere to the substrates or the intrinsic properties of the 2D materials are greatly altered and degraded. Here, we present a residue-free approach for fabricating high-performance graphene devices by patterning a thin film of e-beam resist as a stencil mask. This technique can be generally applied to substrates with varying surface conditions, while causing negligible residues on graphene. The technique also preserves the design flexibility offered by e-beam lithography and therefore allows us to fabricate multi-probe metallic contacts. The graphene field-effect transistors fabricated by this method exhibit smooth surfaces, high mobility, and distinct magnetotransport properties, confirming the advantages and versatility of the presented residue-free technique for the fabrication of devices composed of 2D materials.