Little is known about how the Ediacaran index fossil Cloudina lived and what impact it had on its surroundings. This uncertainty is due to the fact that Cloudina often is preserved with the same mineralogy as the rocks in which it is found; the lack of density contrast means that traditional imaging techniques cannot be used to reconstruct and measure in situ Cloudina populations. Recently, researchers have suggested that Cloudina was a framework reef builder that actively adapted to changing environmental conditions. In this paper, we use a serial grinding and imaging technique to produce 3D models of Cloudina aggregates. Along with detailed field observations, we demonstrate that Cloudina populations are detritus and not in situ growth.The earliest metazoans capable of biomineralization appeared during the late Ediacaran Period (635–541 Ma) in strata associated with shallow water microbial reefs. It has been suggested that some Ediacaran microbial reefs were dominated (and possibly built) by an abundant and globally distributed tubular organism known as Cloudina. If true, this interpretation implies that metazoan framework reef building—a complex behavior that is responsible for some of the largest bioconstructions and most diverse environments in modern oceans—emerged much earlier than previously thought. Here, we present 3D reconstructions of Cloudina populations, produced using an automated serial grinding and imaging system coupled with a recently developed neural network image classifier. Our reconstructions show that Cloudina aggregates are composed of transported remains while detailed field observations demonstrate that the studied reef outcrops contain only detrital Cloudina buildups, suggesting that Cloudina played a minor role in Ediacaran reef systems. These techniques have wide applicability to problems that require 3D reconstructions where physical separation is impossible and a lack of density contrast precludes tomographic imaging techniques.