Research addressing the implications of forest harvesting for mammals has focused on different categories of silvicultural prescriptions. However, the effects of these prescriptions on forest structure can vary considerably, and categories of prescriptions rarely incorporate the market for which timber is being harvested. The latter information is important given the recent shift from conventional round-wood harvesting to wholetree removal for biofuels production, and corresponding reductions in post-harvest woody biomass left on-site. Our goal was to assess the effects of forest harvesting for biofuels on mammal species. Objectives included 1) evaluating how structural components influenced mammals, and 2) assessing the role of scale on species-habitat relationships. We sampled mammals in a 97-ha area of hardwood forest in the Adirondack Mountains in New York that had been partially harvested for biofuels in 2010. We used Sherman traps and track plates to assess the distribution of mammals. We captured 6 species of mammals in Sherman traps and identified 8 species using track plates. Mammalian species varied in their sensitivity to changes in habitat characteristics associated with biofuels harvest (coarse woody debris and slash). Our study reveals a complex suite of factors driving the response of mammals to variation in forest structure as a result of biofuels production. The harvesting practices used in the focal region are unlikely to lead to dramatic changes in the abundance and distribution of individual species of small mammals, but may influence the occurrence of common species including deer-mice and voles.