Using a newly developed fully automated serial-sectioning three-dimensional (3D) microscope, Genus-3D, and a conventional dual-beam SEM, we examined ferrite-martensite dual-phase and eutectoid pearlite microstructures. In particular, we consider the topology and differential geometry. Genus, Euler characteristics, Gaussian curvature, and mean curvatures were obtained from 3D reconstructions. A variation in the martensite morphology in dual-phase steel, i.e., connectivity, was examined to understand the ductile fracture mechanism. In addition, we investigated the 3D morphological variation of lamellar cementite in pearlite during spheroidizing. This 3D observation revealed many holes and fissures in cementite lamellae, which potentially accelerate the spheroidization. The disintegration of lamellar structure into particles was discussed with respect to surface area change per unit volume and local surface morphology (i.e., curvature).