Polymer crystals are metastable and exhibit morphological changes when being annealed. To observe morphological changes on molecular scales we started from small nanometer-sized crystals of highly folded long-chain polymers. Micron-sized stripes consisting of monolayers or stacks of several layers of flat-on oriented polyethylene nanocrystals were generated via evaporative dewetting from an aqueous dispersion. We followed the morphological changes in time and at progressively higher annealing temperatures by determining the topography and viscoelastic properties of such assemblies of nanocrystals using atomic force microscopy. Due to smallness and high surface-to-volume ratio of the nanocrystals, already at 75 °C, i.e. about 60 degrees below the nominal melting point, the lateral size of the crystal coarsened. Intriguingly, this occurred without a noticeable reduction in the number of folds per polymer chain. Starting at around 110 °C, chain folds were progressively removed leading to crystal thickening. At higher temperatures, but still below the melting point, prolonged annealing allowed for surface diffusion of molten polymers on the initially bare substrate, leading eventually to the disappearance of crystals. We compared these results to the behavior of the same nanocrystals annealed in an aqueous dispersion and to bulk samples.