Many microscopy studies require reconstruction from serial sections, a method of analysis that is sometimes difficult and time-consuming. When each section is cut, mounted and imaged separately, section images must be montaged and realigned to accurately analyse and visualize the three-dimensional (3D) structure. Reconstruct is a free editor designed to facilitate montaging, alignment, analysis and visualization of serial sections. The methods used by Reconstruct for organizing, transforming and displaying data enable the analysis of series with large numbers of sections and images over a large range of magnifications by making efficient use of computer memory. Alignments can correct for some types of non-linear deformations, including cracks and folds, as often encountered in serial electron microscopy. A large number of different structures can be easily traced and placed together in a single 3D scene that can be animated or saved. As a flexible editor, Reconstruct can reduce the time and resources expended for serial section studies and allows a larger tissue volume to be analysed more quickly.