Three dimensional Electron Microscopy (EM) and in particular single particle reconstruction using cryo-EM, has rapidly advanced over recent years, such that increasingly several macromolecular complexes can be resolved at subnanometer resolution (6-10 Å). This paper reviews some of the main volumetric image and geometric post-processing steps once a three dimensional EM map (henceforth a 3D map) has been reconstructed from single particle Cryo-EM, as essential steps in an enhanced and automated computational structure interpretation pipeline. In particular the paper addresses automated filtering, critical point calculations, symmetric and non-symmetric molecular domain segmentation, molecular surface selection, curation, and protein secondary structure (α- helices and β-sheets) elucidation from 3D maps.