We investigate the skyrmion formation process in nano-structured FeGe Hall-bar devices by measurements of topological Hall effect, which extracts the winding number of a spin texture as an emergent magnetic field. Step-wise profiles of topological Hall resistivity are observed in the course of varying the applied magnetic field, which arise from instantaneous changes in the magnetic nano-structure such as creation, annihilation, and jittering motion of skyrmions. The discrete changes in topological Hall resistivity demonstrate the quantized nature of emergent magnetic flux inherent in each skyrmion, which had been indistinguishable in many-skyrmion systems on a macroscopic scale.