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We study the structure formation of 1,4,5,8-naphthalenetetracarboxylicacid-
dianhydride (NTCDA) multilayer films on Ag(111) surfaces by energy dispersive near-edge x-ray absorption fine-structure spectroscopy (NEXAFS) and photoelectron spectroscopy. The time resolution of seconds of the method allows us to identify several sub-processes, which occur during the post-growth three-dimensional structural ordering, as well as their characteristic time scales. After deposition at low temperature the NTCDA molecules are preferentially flat lying and the films exhibit no long-range order. Upon annealing the molecules flip into an upright orientation followed by an aggregation in a transient phase which exists for several minutes. Finally, threedimensional islands are established with bulk-crystalline structure involving substantial mass transport on the surface and morphological roughening. By applying the Kolmogorov–Johnson–Mehl–Avrami model the activation energies of the temperature-driven sub-processes can be derived from the time evolution of the NEXAFS signal.