Toward the end of the Pleistocene, the world experienced a mass extinction of megafauna. In North America these included its proboscideans—the mammoths and mastodons. Researchers in conservation biology, paleontology, and archaeology have debated the role played by human predation in these extinctions. They point to traces of human butchery, such as cut marks and other bone surface modifications (BSM), as evidence of human-animal interactions—including predation and scavenging, between early Americans and proboscideans. However, others have challenged the validity of the butchery evidence observed on several proboscidean assemblages, largely due to questions of qualitative determination of the agent responsible for creating BSM. This study employs a statistical technique that relies on three-dimensional (3D) imaging data and 3D geometric morphometrics to determine the origin of the BSM observed on the skeletal remains of the Bowser Road mastodon (BR mastodon), excavated in Middletown, New York. These techniques have been shown to have high accuracy in identifying and distinguishing among different types of BSM. To better characterize the BSM on the BR mastodon, we compared them quantitatively to experimental BSM resulting from a stone tool chopping experiment using “Arnold,” the force-calibrated chopper. This study suggests that BSM on the BR mastodon are not consistent with the BSM generated by the experimental chopper. Future controlled experiments will compare other types of BSM to those on BR. This research contributes to continued efforts to decrease the uncertainty surrounding human-megafauna associations at the level of the archaeological site and faunal assemblage—specifically that of the BR mastodon assemblage. Consequently, we also contribute to the dialogue surrounding the character of the human-animal interactions between early Americans and Late Pleistocene megafauna, and the role of human foraging behavior in the latter’s extinction.