Four groups of transmission electron microscopy (TEM) specimens of Zr52.5Cu17.9Ni14.6Al10Ti5 metallic glass were prepared by double-jet electropolishing, dimpling and ion milling. TEM observations indicate that the microstructures in electron-transparent areas change sensitively with ion milling conditions. Detailed comparisons between the selected area electron diffraction patterns of TEM specimens and the X-ray diffraction patterns of thermally annealed samples of the same composition show that significant heating effects exist in some severe milling processes, resulting in the formation of various ordered structures in thin areas. In TEM specimens prepared by intentionally long time ion milling, the peak temperature locally reached is estimated as high as 780 K, far above the glass transition temperature of this metallic glass. The results suggest that precautions must be taken to prepare TEM specimens of amorphous alloys by ion milling, particularly when the induced microstructure changes may lead to invalid judgments