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We report on the effect of in situ focused ion beam (FIB) trimming on the spin configurations of the hexagonal-shaped elements, characterized by scanning electron microscopy with polarization analysis (SEMPA) imaging. The use of SEMPA and successive in situ FIB trimming makes it possible to study the effect of thickness on the spin configuration of a same hexagonal dot array, eliminating the effect of irregularity in edges caused by the fabrication processes. The results obtained indicate that there exists a transition of a single vortex state to a stable double vortex state when the thickness is reduced to below 8 nm. Micromagnetic modeling has been performed to investigate the effect of reductions in both the thickness and saturation magnetization due to FIB trimming.