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We discuss the formation and post-deposition instability of nanodrop-like structures in thin films of PDIF-CN2 (a perylene derivative) deposited via supersonic molecular beam deposition technique on highly hydrophobic substrates at room temperature. The role of the deposition rate on the characteristic lengths of the organic nanodrops has been investigated by a systematic analysis of atomic force microscope images of the thin films and through the use of the height-height correlation function. The nanodrops appear to be a metastable configuration for the freshly-deposited films. For this reason, post-deposition wetting effect has been examined with unprecedented accuracy throughout a year of experimental observations. The observed time scales, from few hours to months, are related to the growth rate, and characterize the thin films morphological reordering from three-dimensional nanodrops to a well-connected terraced film. While the interplay between adhesion and cohesion energies favors the formation of 3D-mounted structures during the growth, wetting phenomenon following the switching off of the molecular flux is found to be driven by an instability. A slow rate downhill process survives at the molecular flux shutdown and it is accompanied and maybe favored by the formation of a precursor layer composed of more lying molecules. These results are supported by simulations based on a non-linear stochastic model. The instability has been simulated, for both the growth and the post-growth evolution. To better reproduce the experimental data it is needed to introduce a surface equalizer term characterized by a relaxation time taking into account the presence of a local mechanism of molecular correlation.