3D Method denotes that "Differentiated education by Differentiated teachers with Differentiated materials". As mentioned in the theories like "Tiered Education", "Differentiated Learning" and "Multiple Intelligence Theory", taking care of differences of individuals are becoming more important. Not only students, but also teachers are different individuals and need to be trained by giving a chance to show their differences. Besides that, these different teachers need different educational software when teaching the different students. In this specific study, we organized a course to senior students of Math Education in Istanbul University and encourage the students to develop a sample of educational software. In this paper, the problems about designing this type of courses will be discussed, we will share our experiences gained in this study and make suggestions to solve the possible problems and to design more effective "Computer Based Math Instruction" courses.