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Magnetism of oxide antiferromagnets (AFMs) has been studied in single crystals and extended thin films. The properties of AFM nanostructures still remain underexplored. Here, we report on the fabrication and magnetic imaging of granular 100-nm-thick magnetoelectric Cr$_2$O$_3$ films patterned in circular bits with diameters ranging from 500 down to 100 nm. With the change of the lateral size, the domain structure evolves from a multidomain state for larger bits to a single domain state for the smallest bits. Based on spin-lattice simulations, we show that the physics of the domain pattern formation in granular AFM bits is primarily determined by the energy dissipation upon cooling, which results in motion and expelling of AFM domain walls of the bit. Our results provide a way towards the fabrication of single domain AFM-bit-patterned memory devices and the exploration of the interplay between AFM nanostructures and their geometric shape.