Virtual models are a common instructional tool used in chemistry education to help students learn about the 3D structure of molecules. The present study examined effects of two interface design features on participant performance during a molecule orientation task. The features examined were 1) colocation of the visual and haptic workspace and 2) stereoscopic viewing. The results indicate that colocating the interface increased participant accuracy, while providing stereo did not. Neither factor affected response time. The effects of colocation were also reflected in subjective ratings of task demand measured by the NASA-TLX. Spatial ability was predictive of task performance but did not interact with interface effects. The findings are discussed in the context of spatial cognition and interface design for manipulating virtual objects.