Although complex geometries are attainable with additive manufacturing (AM), a major barrier preventing its use in mission-critical applications is the lack of geometric accuracy of AM parts. Existing geometric dimensioning and tolerancing (GD&T) characteristics are defined based on simple landmark features, and thus, need to be customized to capture the subtle difference in parts with complex geometries. Hence, the objective of this work is to quantify the geometric deviations of additively manufactured parts from a large data set of laser-scanned coordinates using an unsupervised machine learning (ML) approach called the self-organizing map (SOM). The central hypothesis is that clusters recognized by the SOM correspond to specific types of geometric deviations, which in turn are linked to certain AM process conditions. This hypothesis is tested on parts made while varying process conditions in the fused filament fabrication (FFF) AM process. The outcomes of this research are as follows: (1) visualizing and quantifying the link between process conditions and geometric accuracy in FFF and (2) significantly reducing the amount of point cloud data required for characterizing of geometric accuracy. The significance of this research is that this unsupervised ML approach resulted in less than 3% of over 1 million data points being required to fully quantify the part geometric accuracy.