Design thinking has an important role in STEM education. However, there has been limited research on how students engage in various modalities throughout the design process in hands-on design tasks. To promote middle school students' engineering literacy, it is necessary to examine the use of design modalities during design. Using a case study approach, we examine middle school students' design stages and modalities during design activities. We also identify the patterns of design processes in the teams with different design outcomes. Drawing on theories in design thinking and embodied interaction, we proposed a framework and devised a video analysis protocol to examine students' design stages and modalities. Middle school students attending a design workshop engaged in two design activities in teams of 3-4 people. The design sessions were video recorded and analyzed using the video analysis protocol. The teams engaged in the stages of planning, building, and testing, while employing the verbal, the visual, and the physical modalities. The teams that varied in design outcomes exhibited different patterns in the use of multiple modalities during the design stages. This study contributes to research on design thinking by proposing a framework for analyzing middle school students' multimodal design processes and presenting data visualization methods to identify patterns in design stages and modalities. The findings suggest the necessity to examine students' use of design modalities in the context of design stages and imply the potential benefits of using multiple modalities during design. The implications for future research and education practices are also discussed.