Abstract The controlled assembly of nanostructures via shape instability mechanisms is a potential alternative to traditional top-down processes like e-beam lithography for nanostructuring surfaces. In this contribution, the dynamics of the nanostructuresʼ assembly via thin film agglomeration have been analyzed. Pt thin films with a thickness of 50 nm were deposited via magnetron sputtering on yttria-stabilized zirconia (YSZ) single crystals and subjected to heat treatments at 1023 K for times ranging from 10 to 130 min. The morphological evolution of Pt thin films has been investigated by means of scanning electron microscopy (SEM) and atomic force microscopy (AFM), obtaining the hole growth dynamics and morphological parameters like the lateral correlation length and the nanostructuresʼ Minkowski functionals. The experimentally obtained morphology evolution is compared to the simulated evolution of thin film structures resulting from a cell dynamical system (CDS) model. Three main observations have been made. (i) The hole radius is found to scale as function of time t with a rate proportional to t − 3 4 [ log 3 t ] . This is in agreement with Srolovitzʼs instability theory describing hole growth predominated by surface diffusion. (ii) The morphological evolution of the Pt thin films has been analyzed as function of time t by means of Minkowski measures and the lateral correlation length. A discontinuity in the lateral correlation length and a significant deviation of the Minkowski functionals from the expected Gaussian behavior was found to be coupled with the coalescence of holes. (iii) By using the Ginzburg–Landau equation for the description of the fundamental diffusion process, the CDS model allows a computational reproduction of the experimentally obtained film morphologies in the early stages of agglomeration.