Thesis development proves most complicated for students, as it implies more than one final work product and involves facing deadlines. One of the most challenging aspects here is writing the thesis paper. Software engineering is marked by specific difficulties, since students focus on the software development and neglect other aspects, first of all, the thesis paper writing. Hence thesis paper writing demands significant support from the university. This paper presents a method of managing the thesis paper writing process for software engineering undergraduates. Mind mapping is used for the early design, fast feedback, and a wide discussion of the thesis paper plans. The method is implemented as a one semester course for last year undergraduates. The evaluation conducted indicates a significant increase in the quality of thesis papers.