The current scripts utilize a well-known cluster analysis algorithm, called ordering points to identify the clustering structures (OPTICS), and an automatic cluster extraction algorithm for clustering analysis of 3D spatial data, specifically for the Atom Probe Tomography data. A hierarchical clustering scheme, together with density-based clustering, were implemented. The advantages of the developed algorithm is that the produced a hierarchy of clusters, which can be retrieved and re-analyzed later, could save researchers time in manually exploring parameter space as in current widely used method, and the capability to identify clusters of varying atomic density in a single run. The current developed scripts can also serve as a platform to test new algorithms with the internal and external APT experts.