The main idea to create virtual organizations lies in the formation of a technical environment unified by merging organizational and informational resources temporarily employed various businesses to increase their business efficiency and competitiveness. Virtual enterprises are a new form of business organization geared towards establishing a new mechanism of market competition, especially for small and medium enterprises that aim to achieve a high technology production. Complexity in the formation of virtual enterprise management system is motivated by the need to find a compromise between the overall presentation of the object complex and detailed description of its components in the development and implementation of the project. This task can be solved with the help of models that meet multi-level methodology focused on presenting stratified design process and tracking problems that occur during the creation of virtual organization management system.