Ultrafast high energy electron diffraction in reflection geometry is employed to study the structural dynamics of self-organized Germanium hut-, dome-, and relaxed clusters on Si(001) upon femtosecond laser excitation. Utilizing the difference in size and strain state the response of hut- and dome clusters can be distinguished by a transient spot profile analysis. Surface diffraction from {105}-type facets provide exclusive information on hut clusters. A pixel-by-pixel analysis of the dynamics of the entire diffraction pattern gives time constants of 40, 160, and 390 ps, which are assigned to the cooling time constants for hut-, dome-, and relaxed clusters.