A technique for preparation of a pillar shaped sample and its multi-directional observation of the sample using a focused ion beam (FIB) / scanning transmission electron microscopy (STEM) system has been developed. The system employs an FIB/STEM compatible sample rotation holder with a specially designed rotation mechanism, which allows the sample to be rotated 360 degrees [1-3]. This technique was used for the three dimensional (3D) elemental mapping of a contact plug of a Si device in 90 nm technology. A specimen containing a contact plug was shaped to a pillar sample with a cross section of 200 nm x 200 nm and a 5 um length. Elemental analysis was performed with a 200 kV HD-2300 STEM equipped with the EDAX genesis Energy dispersive X-ray spectroscopy (EDX) system. Spectrum imaging combined with multivariate statistical analysis (MSA) [4, 5] was used to enhance the weak X-ray signals of the doped area, which contain a low concentration of As-K. The distributions of elements, especially the dopant As, were successfully enhanced by MSA. The elemental maps were reconstructed from the maps.