This research aims to determine the opinions of prospective science teachers regarding structured, semi-structured and unstructured three-dimensional modeling processes according to several problems. Thus, modeling activities were conducted in three different process as structured (problem+materials+process), semistructured (problem+materials) and unstructured (problem). In this research planned within the framework of embedded multiple case study design, a total number of 67 prospective science teachers created six models concerning human circulation and respiratory system. "Focus Group Discussions," "Video Recordings," and "Model-Related Activity Documents" were used as data collection tools. The collected data were analyzed comparatively using the content analysis method. Five themes, which are a) challenges encountered, b) contributions, c) availability, d) alternative ideas and e) originality, were found to be common in all modeling groups. In general, it was determined that modeling activities had some positive impacts such as supporting learning theoretical information, enabling information to be remembered easily, ensuring the recognition of incomplete information and learning by doing and supporting learning in a fun environment. As a negative impact, on the other hand, it was concluded that it was a hard and tiring task to attach materials during modeling activities.