Deep neural networks provide a promising tool for incorporating semantic information in geometry processing applications. Unlike image and video processing, however, geometry processing requires handling unstructured geometric data, and thus data representation becomes an important challenge in this framework. Existing approaches tackle this challenge by converting point clouds, meshes, or polygon soups into regular representations using, e.g., multi-view images, volumetric grids or pla- nar parameterizations. In each of these cases, geometric data representation is treated as a fixed pre-process that is largely disconnected from the machine learning tool. In contrast, we propose to optimize for the geometric representation during the network learning process using a novel metric alignment layer. Our approach maps unstructured geometric data to a regular domain by minimizing the metric distortion of the map using the regularized Gromov–Wasserstein objective. This objective is parameterized by the metric of the target domain and is differentiable; thus, it can be easily incorporated into a deep network framework. Furthermore, the objective aims to align the metrics of the input and output domains, promoting consistent output for similar shapes. We show the effectiveness of our layer within a deep network trained for shape classification, demonstrating state-of-the-art performance for nonrigid shapes.