Transmission electron microscope (TEM) is an excellent tool for studying the structure and properties of nanostructured materials. As the development of $C_s$-corrected TEM, the direct analysis of atomic structures of nanostructured materials can be performed in the high-resolution transmission electron microscopy (HRTEM). Especially, fast Fourier transform (FFT) technique in image processing is very useful way to determine the crystal structure of HRTEM images in reciprocal space. To apply FFT technique in HRTEM analysis in more reasonable and friendly manner, we made a new circular region of interest (C-ROI) FFT script and tested it for several HRTEM analysis. Consequentially, it was proved that the new FFT application shows more quantitative and clearer results than conventional FFT script by removing the streaky artifacts in FFT pattern images. Finally, it is expected that the new FFT script gives great advantages for quantitative interpretation of HRTEM images of many nanostructured materials.