There has been much interest in using software tools to scaffold learners in complex tasks, that is, to provide supports that enable students to deal with more complex content and skill demands than they could otherwise handle. Many different approaches to scaffolding techniques have been presented in a broad range of software tools. I argue that two complementary mechanisms can explain how a diversity of scaffolding approaches in software act to support learners. Software tools can help structure the learning task, guiding learners through key components and supporting their planning and performance. In addition, tools can shape students' performance and understanding of the task in terms of key disciplinary content and strategies and thus problematize this important content. Although making the task more difficult in the short term, by forcing learners to engage with this complexity, such scaffolded tools make this work more productive opportunities for learning. I present arguments for these mechanisms in terms of the obstacles learners face, and I present several brief examples to illustrate their use in design guidelines. Finally, I examine how the mechanisms of structuring and problematizing are sometimes complementary and sometimes in tension in design, discuss design tradeoffs in developing scaffolded investigation tools for learners, and consider the reliance of scaffolding on a classroom system of supports.