This research investigates the role of interface manipulation style on reflective cognition and concept learning through a comparison of the effectiveness of three verisons of a software application for learning two-dimensional transformation geometry. The three versions respectively utilize a Direct Object Manipulation (DOM) interface in which the user manipulates the visual representation of objects being transformed; a Direct Concept Manipulation (DCM) interface in which the user manipulates the visual representation of the transformation being applied to the object; and a Reflective Direct Concept Manipulation (RDCM) interface in which the DCM approach is extended with scaffolding. Empirical results of a study showed that grade-6 students using the RDCM version learned significantly more than those using the DCM version, who is turn learned significantly more than those using the DOM version. Students using the RDCM version had to process information consciously and think harder than those using the DCM and DOM versions. Despite the relative difficulty when using the RDCM interface style, all three groups expressed a similar (positive) level of liking for the software. This research suggests that some of the educational deficiencies of Direct Manipulation (DM) interfaces are not necessarily caused by their “directness,” but by what they are directed at—in this case directness toward objects rather than embedded educational concepts being learned. This paper furthers our understanding of how the DM metaphor can be used in learning- and knowledge-centered software (i.e., learnware) by proposing a new DM metaphor (i.e., DCM), and the incorporation of scaffolding to enhance the DCM approach to promote reflective cognition and deep learning.