In this paper, the inversion algorithm based on graph theory is applied on three real gravity data sets. The goal, here, is to use this new inversion algorithm to model the skeleton of these subsurface targets by an ensemble of similar point masses. Here, model parameters are the Cartesian coordinates of the point masses and their total mass. The set of point masses is associated with a complete weighted graph and Kruskal’s algorithm is used to solve the minimum spanning tree (MST) problem for the graph, yielding a stabilizer which is called “equidistance function”. This function leads to a homogeneous spatial distribution of connected point masses, consequently, a skeleton of the subsurface body. The methodology provides suitable information about the extent of the bodies in east and depth directions.