Cathodoluminescence (CL) imaging and spectroscopy, as well as backscattered electron imaging, were used to assign the occurrence of several mineral phases and rock structures in altered nordmarkites and calcite-bearing granites from the Nb-Zr-REE deposits from Khaldzan Buregte and Tsakhir (Mongolian Altai) to three events: (1) intrusion of barren nordmarkites; (2) intrusion of small bodies of calcite-bearing granites with metasomatic alteration of the wall-rocks; and (3) alteration by F-rich fluids. Unusual red and yellow CL caused by Fe (super 3+) and Mn (super 2+) emission centres were detected in microcline and albite. Fe (super 3+) centres were also established (along with others) in quartz, zircon, and possibly in fluorite. Magmatic and metasomatic rock structures and internal structures of the minerals coexist in the samples. The primary magmatic features were in part preserved during alteration. In contrast, the internal and the centre structures may be changed during alteration even in non-replaced mineral phases. Euhedral minerals may be formed by secondary processes as shown for lath-shaped albite. The occurrence of pseudomorphs, the inheritance of elements during replacement, and the mechanical effects of secondary minerals on earlier mineral phases during metasomatic growth are proposed as criteria for the reconstruction of the mineral succession in altered rocks. Snowball structures may be formed as a result of metasomatic alteration rather than as a magmatic intergrowth.