A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 Cryo-EM maps with resolutions of 4.5 angstrom or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 Cryo-EM Model Challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 angstrom-2.1 angstrom.