Electric, magnetic or mechanical properties of materials have tight relation with surface and interior three dimensional (3D) structures of them. Thus, understanding the correlation of properties and material structure is crucial to develop and to improve high-performance materials. The SPM (Scanning Probe Microscopy) is technique for quantitative atomic-level measurement of specimen surface feature with electrical or mechanical properties simultaneously. While the SEM (Scanning Electron Microscopy) is technique for observation of surface structure, composition, crystalline and element distributions. Recently, 3D structural analysis method (reconstructed from serial section images can be collected by repetition of FIB slice and SEM observation/analysis) [1] is often used especially with FIB (Focused Ion Beam) and SEM composite instrument.