We applied the zone heating method to cylinder-forming diblock copolymers (bcp) for controlling the orientation of the hexagonally packed cylindrical microdomain structures (hex-cyl) and reported the results of the structure analysis by small-angle X-ray scattering (SAXS) in our previous paper [Mita et al. Macromolecules 2007, 40, 5923]. In this report, we present the results of the real-space analysis of the zone-heated bcp by using polarized optical microscopy and transmission electron microscopy. The real-space analysis elucidated that the zone heating creates the columnar-shaped grains extending along the temperature gradient (del T) direction: within a given grain the cylinder axes are aligned perpendicular to del T axis with a fixed rotational angle phi around del T axis: the angle phi varies statistically randomly over many grains. These results firmly verified the columnar grain model proposed by the previous Fourier-space analysis. Furthermore, the real-space analysis elucidated the average lateral size and shapes of the grains, the commensuration of the hex-cyl at the grain boundaries, and the fact that this commensuration was achieved by the distortion of the domain spacing of the hex-cyl near the grain boundaries from its equilibrium value.