The visualization and representation competencies in engineering and design education foster a comprehensive grasp of learning design elements and principles, problem-solving, and confidence amongst many other foundation skills (Goldsmith et al. in Psychol Aesthet Creat Arts 10:56–71, 2016 [1]; Hsi et al. in J Eng Educ 86:151–158, 1997 [2]). To ensure effective design education, it is crucial to establish a pedagogical structure based on student experiences and empathetic teaching practices. Our paper focuses on developing such strategies for 3D visualization, particularly in the context of teaching clay modelling to first- and second-year undergraduate design students. The study examines practices and challenges faced by novice students during a clay modelling assignment. We analysed the initial ideas, detailed sketches, and final clay models of hundred undergraduate design students. We systematically examined each stage of the design process from initial sketches followed by decoding into basic 3D forms, identifying the base form, adding subsidiary forms, and incorporating finer details and identified gaps between students’ final clay models and the expected learning outcomes. We observed that students faced difficulties translating their 2D drawings into 3D clay forms. To understand their design practices and perspectives, we further engaged in focused discussions with twenty first-year undergraduate students. These conversations were transcribed and examined to determine students’ misconceptions and erroneous beliefs regarding modelling along with identifying their challenges while transitioning from 2D drawing to 3D modelling. Our preliminary analysis uncovered differences between this transition, especially regarding specific details such as elements of form, principles of space, proportion, and balance that define the characteristic features of a 3D model. These findings highlight the importance of enhancing spatial awareness among novice design students. This paper, therefore, explores relevant design instruction that can facilitate and ease the 3D visualization process.