Control and understanding of ensembles of skyrmions is important for realization of future technologies. In particular, the order-disorder transition associated with the 2D lattice of magnetic skyrmions can have significant implications for transport and other dynamic functionalities. To date, skyrmion ensembles have been primarily studied in bulk crystals, or as isolated skyrmions in thin film devices. Here, we investigate the condensation of the skyrmion phase at room temperature and zero field in a polar, van der Waals magnet. We demonstrate that we can engineer an ordered skyrmion crystal through structural confinement on theμm scale, showing control over this order-disorder transition on scales relevant for device applications.