A focused Ga⁺ ion beam (30 keV and 187 pA) have been irradiated at doses of 8.92×10¹⁶–2.68×10¹⁸ ions/cm² in (001) plane of a single-crystalline Ni and an amorphous Ni₇₅B₁₅Si₁₀ alloy and their surface evolution was investigated by atomic force microscopy. The root-mean-square (rms) roughness increased with increasing ion dose and the transition of surface morphology from dot structure to ripple structure occurred during FIB machining in the single-crystalline Ni. However, the amorphous Ni₇₅B₁₅Si₁₀ alloy showed no such transition of surface morphology and held the rms roughness almost constant in an ion dose range more than about 1×10¹⁷ ions/cm². Therefore, it is suggested that surface diffusion, which is the primary smoothing mechanism for crystalline surfaces, plays an important role in smoothening during FIB machining when the ion dose is low, while viscous flow, which is dominant for amorphous surfaces, contributes to smoothening when the ion dose is large.