We found appropriate femtosecond laser irradiation conditions to locally melt Au/Ni double-layered thin films deposited on a GaN layer. The laser irradiation of the Au/Ni films was carried out through GaN and transmission electron microscopy revealed that GaN acted as a tough window to introduce laser pulses without suffering laser-induced damages. The Au/Ni double-layered thin films melted along the laser-irradiation lines and re-solidified into coarse particles containing an Au–Ni solid solution phase. On the other hand, in the area between laser-modified regions, the Au/Ni thin films retained the same morphology as the as-deposited state. The transition from the melted region to the unaffected area occurred in a narrow intermediate region. The present results show a possibility of a novel technique to site-specifically melt thin films to form a solid solution phase by femtosecond laser irradiation.