The morphological architecture and distribution of modern and ancient carbonate systems has been shown to follow spatial-self-organization, however, limited studies describe the morphometrics of microbial carbonates. Upper Cambrian microbial-build-ups outcropping in Central Texas, are exposed laterally (plan view), enabling a study of their morphological architecture and spatial distribution. Drone imagery was acquired to capture the outcrop features and develop a digital terrain model (cm scale resolution) for a bedding plane outcrop (600 × 200 m in size). Four scales of microbial growth (S1- few dm, S2- few m, S3- few tens of m, and S4- few hundreds of m) were identified and mapped. A series of morphometric analysis including Ripley's k, univariate, multivariate, and grouping were conducted and results demonstrate that, the scales S1, S2, and S3 display clustering and the spatial organization of microbial-buildups is naturally organized and not random. Further, as the size of the build-ups increases (from S1–S4), the anisotropy (length/width) increases, their shape becomes oblong, and they become aligned (S2–S4) with the inferred regional winds and tide-associated currents (NE-SW according to the present geography). The S1 scale does not align itself with the regional currents; instead, the build-ups behaved as a baffle during growth, and modified the currents locally, leading to preferential alignment at the edges within S2. As the scales increases in sizes (S2, S3, S4), there is competition for space, and due to regional currents, the larger scales preferentially align parallel to high-energy currents. The trends and spatial relationships identified in this study are particularly relevant and provide a scenario for sub-seismic scale heterogeneities for subsurface microbial hydrocarbon reservoirs.