Mixing of double‐layered Al‐on‐Au and Al‐on‐W structures by a focused ion beam (FIB) has been used to define fine patterns in Au and W layers and to demonstrate that the mixing spread is less than 0.1 μm. Since the mixed Al–Au alloy and Au have higher sputtering yield than Al, etching with 4‐keV Xe ions engraves the FIB‐defined pattern in the Au layer. This process yielded 0.2‐μm‐wide grooves in 20‐nm Al/0.3‐μm Au with a 50‐keV Ga+FIB of ∼5×1015/cm2. In the Al/W, Al is removed in H3PO4leaving the mixed Al–W alloy, which acts as a durable mask in SF6reactive ion etching of W with a selectivity of ∼80. This process enables the Ga+FIB to define patterns less than 0.1 μm in 20‐nm Al/0.3–0.5‐μm W with a sensitivity of ∼1×1015/cm2. To demonstrate applicability of the above processes, patterns of x‐ray masks were fabricated and transferred with synchrotron radiation to poly‐methyl‐methacrylate. Backscattering measurements of He ions and x‐ray diffraction verify mixing occurs within the range of the ion. The process performance and its relation with the mixing kinetics are also discussed.