In programming courses there are various ways in which students attempt to cheat. The most commonly used method is copying source code from other students and making minimal changes in it, like renaming variable names. Several tools like Sherlock, JPlag and Moss have been devised to detect source code plagiarism. However, for larger student assignments and projects that involve a lot of source code files these tools are not so effective. Also, issues may occur when source code is given to students in class so they can copy it. In such cases these tools do not provide satisfying results and reports. In this study, we present an improved process model for plagiarism detection when multiple student files exist and allowed source code is present. In the research in this paper we use the Sherlock detection tool, although the presented process model can be combined with any plagiarism detection engine. The proposed model is tested on assignments in three courses in two subsequent academic years.