An investigation of the spatially resolved distribution of domains in the multiferroic phase of MnWO$_4$ reveals that characteristic features of magnetic and ferroelectric domains are inseparably entangled. Consequently, the concept of multiferroic hybrid domains is introduced for compounds in which ferroelectricity is induced by magnetic order. The three-dimensional structure of the domains is resolved. Annealing cycles reveal a topological memory effect that goes beyond previously reported memory effects and allows one to reconstruct the entire multiferroic multidomain structure subsequent to quenching it.