DeltaViewer is a free three-dimensional image processing program developed especially for researchers in fields of biology, physiology and medicine. It is capable of processing varieties of images from CT, MRI and confocal laser microscopes. DeltaViewer’s powerful image alignment function also allows the user to easily reconstruct 3D images from serial sections obtained by optical and electron microscopes. In this note, we explain in detail using actual examples, how to make successful reconstructions from serial sections.