We report on the formation of homogeneous nanostructures using a two-step ablation process with square flattop beams of femtosecond (fs) laser pulses. The Gaussian beam output from a ytterbium fs laser system was converted to a square flattop beam by a refractive beam shaper and a square mask. This beam was split into two with a diffraction optical element, and then the downsized beams were spatially and temporally superimposed on a titanium surface. In the first step, the interference fringes of these two beams formed grooves with a period of 1.9 µm through ablation. Next, the surface was irradiated at normal incidence by a single beam to form a homogeneous line-like nanostructure with a period of 490 nm in a 53 μm square area. This nanostructure had a constant period and was formed over 95% of the laser-processed area, indicating that the ratio between the nanostructure and modification area was over six times larger than that for a Gaussian beam.