Three-dimensional (3D) pens are emerging educational tools that enable users to create tangible, freeform 3D printed models. However, their pedagogical potential in science education remains underexplored. This study examined preservice teachers' experiences using 3D pens to create models for primary biology and chemistry education, focusing on their development of science skills, perceptions, and problems encountered. Thirty-four Bachelor of Elementary Education (BEEd) pre-service teachers from a state university campus in the Cordillera Administrative Region (CAR), Philippines, participated in a sequential explanatory mixed-method design. Results revealed that the preservice teachers strongly agreed that using 3D pens enhanced their creativity and technological skills. They encountered problems such as the pens' need for a constant power supply, unpleasant filament odors, and difficulty in creating precise and durable models. They noted the lack of skills and mastery in using the pens, as well as the need for extended user practice. This study supports that 3D pens are accessible and innovative tools that can enhance primary biology and chemistry lessons. It further implies that teacher education programs can adopt the pens, equipping future educators with experiential competence in delivering engaging, student-centered science learning.