Many medical image analysis techniques require an initial localization and segmentation of anatomical structures. As part of the VISCERAL benchmarks on Anatomy segmentation, a hierarchical multi-atlas multi-structure segmentation approach guided by anatomical correlations is proposed. The method begins with a global alignment of the volumes and refines the alignment of the structures locally. The alignment of the bigger structures is used as reference for the smaller and harder to segment structures. The method is evaluated in the ISBI VISCERAL testset on ten anatomical structures in both contrast-enhanced and non-enhanced computed tomography scans. The proposed method obtained the highest DICE overlap score for some structures like kidneys and gallbladder. Similar segmentation accuracies compared to the highest results of the other methods proposed in the challenge are obtained for most of the other structures segmented with the method.