3D structures of bulk alloys and nanoparticles have been studied by means of electron tomography using scanning transmission electron microscopy (STEM). In the case of nanoparticles of Fe-Pd alloy, particle size, shape, and locations were reconstructed by weighted backprojection (WBP), as well as by simultaneous iterative reconstruction technique (SIRT). We have also estimated the particle size by simple extrapolation of tilt-series original data sets, which proved to be quite powerful. We demonstrate that WBP yields a better estimation of the particle size in the z direction than SIRT does, while the latter algorithm is superior to the former from the viewpoints of surface roughness and dot-like artifacts. In contrast, SIRT gives a better result than WBP for the reconstruction of plate-like precipitates in Mg-Dy-Nd alloys, in respect of the plate thickness perpendicular to the z direction. We also show our recent results on the 3D-tomographic observations of microstructures in Ti-V-Al, Ti-Nb, Cu-Ag, and Co-Ni-Cr-Mo alloys obtained by STEM tomography.