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The estimation and uncertainty quantification of channelized reservoirs in a data assimilation framework is very hard to achieve due to the geometrical and topological characteristics of the facies fields. The channelized structure is broken after the updated step of the data assimilation process, and this causes unrealistic updated reservoir models. Geological realism can be achieved in two ways, either by learning or by conditional sampling from the prior distribution. In this study, we train a convolutional autoencoder (CAE) to reconstruct the channelized structure of a reservoir with three facies types namely channel, levee, and shale, where there is a topological transition between them. The training is done with a set composed of pairs of images, of which one is perturbed, and the other has a correct geometrical and topological structure. The CAE is linked with a parameterization of the facies fields and became part of it. The enhanced parameterization is further coupled with ES-MDA for history matching. The results show that the updated facies fields keep the prior channelized structure, and the indicators of a good history matching are fulfilled. This means good results in terms of facies estimation, uncertainty quantification, data match, and prediction capabilities of the updated ensemble.