Crystal structure refinement by the convergent-beam electron diffraction (CBED) method has the following advantages: (i) Nanometer-size crystal structure refinement: CBED patterns can be obtained from specimen areas of a few nanometer in diameter, (ii) Dynamical diffraction effect: the CBED intensities contain phase information of crystal structure factors through the strong dynamical effect. (iii) Site-selective analysis: the use of Bloch states formed by incident electrons allows structure determination weighted for specific atom sites. Energy-filtering (EF) to revome inelastically scattered background is now getting necessary for such quantitative analysis of CBED patterns. Especially for the determination of atom positions and Debye-Waller factors, the use of energy-filtered higher-order Laue zone (HOLZ) CBED patterns is essential because small displacements of atoms can be sensitively detected using HOLZ reflections with large reciprocal vectors. For this purpose, we developed a new fl-filter transmission electron microscope (JEM-2010FEF) with a high acceptance angle [2] and a new analysis program “mbfit” to refine structural parameters using many-beam Bloch-wave calculations and least-square fitting [1].