The development of information technologies changes the learning process. The amount of publicly available data of e-learning systems allows personalized studies. Therefore, the tutor sometimes is needed for the student’s evaluation and consultation only. To ensure clear evaluation requirements and objective evaluation process, the learning material, as well as the evaluation system, must be discrete and semantically expressed. The list of mastered competencies and skills is more important to the enterprise; therefore, during the last years, the study process has concentrated on competency evaluation too. However, the current practice, when students’ competencies are summarized and expressed as one quantitative metric (score), do not express the list of students’ competencies and their level. To solve the problem, in this paper, we proposed a method for the design of competencies’ tree. The competency tree has to be formatted based on context modeling principles and analysis of Scope-Commonality-Variability. The usage of competency tree for students’ competencies’ evaluation proposes clearly defined and semantically expressed evaluation method for both human and e-learning evaluation process. This paper presents the results of the empirical experiment to adapt the proposed competency tree design and application for competencies’ e-evaluation method, based on flexibility, adaptability, and granularity of learning material.