Abstract We present a comparative study of the physical properties and the spatial distribution of column density peaks in two Giant Molecular Clouds (GMC), the Pipe Nebula and Orion A, which exemplify opposite cases of star cluster formation stages. The density peaks were extracted from dust extinction maps constructed from Herschel/SPIRE farinfrared images. We compare the distribution functions for dust temperature, mass, equivalent radius and mean volume density of peaks in both clouds, and made a more fair comparison by isolating the less active Tail region in Orion A and by convolving the Pipe Nebula map to simulate placing it at a distance similar to that of the Orion Complex. The peak mass distributions for Orion A, the Tail, and the convolved Pipe, have similar ranges, sharing a maximum near 5 M⊙, and a similar power law drop above 10 M⊙. Despite the clearly distinct evolutive stage of the clouds, there are very important similarities in the physical and spatial distribution properties of the column density peaks, pointing to a scenario where they form as a result of uniform fragmentation of filamentary structures across the various scales of the cloud, with density being the parameter leading the fragmentation, and with clustering being a direct result of thermal fragmentation at different spatial scales. Our work strongly supports the idea that the formation of clusters in GMC could be the result of the primordial organization of pre-stellar material.