Ongoing physics education research (PER) at Grand Valley State University (GVSU) is guiding the development of instructional materials for teaching modern physics. Results from this project can help address the question: To what extent should we expect upper-level physics students to be able to apply concepts previously covered in class—even those addressed through PER-based instruction at the advanced level—to different situations? Extensive research at the introductory level has already revealed that such transfer is extremely difficult for beginning students to do on their own. Preliminary results from this project suggest that, even among upper level students, specific conceptual and reasoning difficulties must be addressed explicitly and at multiple instances during instruction.