In this report, a method is discussed to perform successive milling on yttria-stabilized zirconia (YSZ), NiO-YSZ and Ni-alloy at the intervals of 85 nm 50 nm and 100 nm, respectively using a focused ion beam (FIB) followed by electron backscatter diffraction (EBSD) analysis on each slice. The EBSD data is then reconstructed to generate 3D volume. The 3D-EBSD band quality data is superimposed on inverse pole figure (IPF) grain orientation analysis to get a correlation with quality of band indexing. For the NiO-YSZ case, grain orientations and band quality factors were matched for grains ∼250 nm diameters producing a high resolution 3D-EBSD data. For this case, a pore space in 3D volume was visible due to nanocrystalline NiO-YSZ grain network. The advantages of 3D EBSD are discussed in the context of its applications to SOFC research community.