Crystal structures of MOFs experimentally determined from XRD studies often exhibit artifacts such as missing hydrogen atoms, crystallographic disorder, and unwanted guest molecules in the pores . These artifacts are obstacles to conducting molecular simulations of gas adsorption, which require a chemically valid structure resembling the activated MOF. PoreMatMod.jl can repair these artifacts of XRD to give a simulation-ready crystal structure. Unwanted solvent molecules or adsorbates in the pores of a MOF structure can be removed by searching for the graph of the solvent/adsorbate and replacing it with nothing (i.e., deleting it). To prevent necessary structural components from also being removed, the user may specify an option in the substructure search to return subgraphs of the parent graph that are isomorphic to the query fragment and are disconnected from the remainder of the nodes in the parent graph.