Atomically precise fabrication methods are critical for the development of next-generation technologies. For example, in nanoelectronics based on van der Waals heterostructures, where two-dimensional materials are stacked to form devices with nanometer thicknesses, a major challenge is patterning with atomic precision and individually addressing each molecular layer. Here we demonstrate an atomically thin graphene etch stop for patterning van der Waals heterostructures through the selective etch of two-dimensional materials with xenon difluoride gas. Graphene etch stops enable one-step patterning of sophisticated devices from heterostructures by accessing buried layers and forming one-dimensional contacts. Graphene transistors with fluorinated graphene contacts show a room temperature mobility of 40,000 cm  V  s at carrier density of 4 × 10  cm and contact resistivity of 80 Ω·μm. We demonstrate the versatility of graphene etch stops with three-dimensionally integrated nanoelectronics with multiple active layers and nanoelectromechanical devices with performance comparable to the state-of-the-art.