A novel visualization technique was proposed to extract the three-dimensional vortex structure of a turbulent puff, which is a local turbulence event that is observed in pipe flows at relatively low Reynolds numbers. The technique is based on multi-color illumination of microscopic flakes that are suspended in the flow, which makes structural visualization more informative than conventional monochrome approaches. A special optical arrangement of two laser sheets, colored green and blue, was established for the circular pipe. Based on an image analysis sequence, the internal structure of the puff is reconstructed as a cross-sectional temporal 3D image consisting of voxels with unicolor degrees between green and blue, where an individual single vortex is extracted as a pair of two-color stripes. This allows quantification of the azimuthal wavenumber of the vortical structure that characterizes the puff. The wavenumber results agreed well with the results of previous studies, thus supporting the applicability of the proposed visualization technique.