The purpose of this study was to develop a framework for analyzing and evaluating student-constructed models of physical phenomena and monitoring the progress of these models. Moreover, we aimed to examine whether this framework could capture differences between models created using different computer-based modeling tools; namely, computer-based programming environments which, in prior research, were found to differ in various aspects of the models constructed through them. We analyzed 220 computer-based models of physical phenomena developed by two groups of elementary-school students. Using open coding we developed a framework that includes five elements of scientific models that code for representations of: (i) the physical objects; (ii) the physical entities; (iii) the object behaviors; (iv) the interactions among physical objects, physical entities, and object behavior(s); and (v) the accuracy of the phenomenon depiction. The implementation of this framework confirmed that it can differentiate student-generated models according to their sophistication and structural components, independent of the computer-based programming environments used to create the models. (Contains 2 tables and 2 figures.)