Three-dimensional (3D) microscopy is a new and rapidly expanding area. A DualBeam system, with both a focused ion beam (FIB) column and an electron column, is a powerful instrument for imaging and sectioning microstructures to generate a full 3D sample reconstruction. When an electron backscatter diffraction (EBSD) system is attached to the DualBeam, it becomes a unique tool for making 3D crystallographic measurements on a wide variety of materials. Combining the successive removal by FIB, with sequential EBSD maps taken with the electron beam requires clear geometric considerations and a high level of automation to obtain a decent resolution in the third dimension, including positional sub-pixel re-alignment. Complete automation allows controlled sectioning and analysis of a significant volume of material without operator intervention: a process that may run continuously and automatically for many hours. Using a Nova600, a Channel 6 EBSD system and dedicated control software, Aluminium, Nickel and Steel specimens have been examined and volumes with up to 200 slices have been successfully analysed.