The structural evolution in amorphous silicon and germanium thin films has been investigated by high-resolution transmission electron microscopy (HRTEM) in conjunction with autocorrelation function (ACF) analysis. The results established that the structure of as-deposited semiconductor films is of a high density of nanocrystallites embedded in the amorphous matrix. In addition, from ACF analysis, the structure of a-Ge is more ordered than that of a-Si. The density of embedded nanocrystallites in amorphous films was found to diminish with annealing temperature first, then to increase. The conclusions also corroborate well with the results of diminished medium-range order in annealed amorphous films determined previously by a variable coherence microscopy method.