This paper describes the types of models that biology majors use and how they go about making their models in learning key concepts in biology such as the cell membrane, cytoskeleton and cell structure. Initially, a total of 44 biology students from all year levels enrolled in the second semester of calendar year 2008-2009 were asked to make their respective models of the cell membrane, cytoskeleton and cell structure. They were also asked to answer an open-ended questionnaire. Of the 44, only 20 (five from each year level) were randomly selected for a one-on-one interview. Results showed that the student-generated models from all year levels were mostly analogies, some textbook definitions and occasional drawings. In making their model, students first read the text; second, outline similarities in structure and function or both; and third, make the model. Data suggest that models are good diagnostic tools for identifying critical thinking skills of students. In this case, students mostly demonstrate the ability to recognize similarities in structure and function between the concept and their model. Some senior students demonstrated integration and reflective thinking in making their models. Thus, more opportunities for student-generated models must be available if students were to develop integration and reflective thinking in their models.