Due to the overhead presented by the synthesis, procurement, and screening of chemical libraries, triaged approaches to formulating optimal libraries are desired to alleviate such resource constraints. To this end, we have developed Dedenser which functions by downsampling chemical point clouds to remove molecules from high density regions in chemical space, providing chemical libraries with reduced membership while maintaining diversity. We hope that researchers will find utility in Dedenser, as it can facilitate the generation of uniformly distributed clusters in datasets drawn from irregularly populated chemical space. Additionally, a command line interface tool version of Dedenser allows for researchers to generate, downsample, and visualize chemical point clouds without any need to code. Beyond the explanation for usage described within this manuscript, Dedenser is accompanied by full documentation to assist those that wish to utilize their own chemical point clouds or further modify the code.