Deep learning based pipelines for semantic segmentation often ignore structural information available on annotated images used for training. We propose a novel post-processing module enforcing structural knowledge about the objects of interest to improve segmentation results provided by deep learning. This module corresponds to a ``many-to-one-or-none'' inexact graph matching approach, and is formulated as a quadratic assignment problem. Using two standard measures for evaluation, we show experimentally that our pipeline for segmentation of 3D MRI data of the brain outperforms the baseline CNN (U-Net) used alone. In addition, our approach is shown to be resilient to small training datasets that often limit the performance of deep learning.