A typical dual-beam platform combines a focussed ion beam (FIB) microscope with a field emission gun scanning electron microscope (FEGSEM). Using this platform, it is possible to sequentially mill off > ~ 50 nm slices of a material by FIB and characterise, at high resolution, the crystallographic features of each new surface by electron backscatter diffraction (EBSD). The successive images can be combined to generate 3-D crystallographic maps of the microstructure. This paper describes various aspects of 3-D FIB tomography in the context of understanding the microstructural evolution of metals during deformation and annealing. The first part of the paper describes the influence of both metal type and milling parameters on the quality of EBSD patterns generated from a surface prepared by FIB milling. Single crystals of some face centred cubic metals were examined under varying FIB milling parameters to optimise EBSD pattern quality. It was found that pattern quality improves with increasing atomic number with the FIB milling parameters needed to be adjusted accordingly. The second part of the paper describes a useful technique for FIB milling for the reliable reconstruction of 3-D microstructures using EBSD. There is an initial procedure involving extensive milling to generate a protruding rectangular-shaped volume at the free surface. Serial sectioning is subsequently carried out on this volume. The technique was used to investigate the recrystallization behaviour of a particle-containing nickel sample, which revealed a number of features of the recrystallizing grains that are not clearly evident in 2-D EBSD micrographs.