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The effectiveness of a Master’s Program Course can only be appraised with the support of an efficient and accurate evaluation program. Taking the Problem Based Learning, as a reference to implement practical and real problems on a class of master students, and the traditional methods that focuses on formal exams as methodology, a method for evaluation was defined to contemplate both scopes. Nevertheless, such method was first applied in a case study of CESAR.edu Master’s Program Class and is being continuously used and improved in order to support the students learning process, providing quantitative results so that they can evaluate and progress their performance along the course. Software Engineering is the core discipline that guides the program, and the implementation of Software Factories is the mean to provide the Problem Based structure in the context of a masters program.