The integration of 3D models in biology education has demonstrated significant potential in enhancing student learning experiences and understanding of complex biological concepts. This study aims to determine the effect of the 3D “Nephron Model” used in the 11th grade biology course on students’ understanding of micro-scale topics in biology discipline and their opinions about the model. This study, which covers an application carried out for four lesson hours with the participation of 20 students in the eleventh grade, was conducted using the case study method in order to describe and analyze a limited system in depth. During the application, the nephron model, which was designed by the researchers and five biology teachers during the project process and printed out with a 3D printer, was used. The first version of the model was used in a two-hour lesson. After the first application, the second version of the model, which was revised in line with student opinions, was used in the other two-hour lesson process. The data obtained in this context were analysed by content analysis. After the lessons, the students answered the questions in the reflective writing form presenting their opinions about the model and the lesson and filled in the “Model Evaluation Rubric” to evaluate the model. Student opinions revealed that the revised version of the model should be improved in terms of size, durability and colour. The design and functionality of the revised model enriched the learning process and made the students and the teacher more interactive.