The need to reduce a gap between organizational context and technology within enterprise has been recognized and discussed by both researchers and practitioners. In order to solve this problem it is required to capture and analyze both business and IT dimensions of enterprise operation. In this regard, Enterprise Modeling is currently considered as widely used and powerful tool that enables and facilitates alignment of business with IT. The central role of EM process is EM practitioner - a person who facilitates and drives EM project towards successful achievement of its goals. Conducting EM is a highly collaborative and nontrivial process that requires considerable skills and experience since there are various challenges to manage and to deal with during the whole EM project. Despite quite wide range of related research, the question of EM challenges needs further investigation, in particular concerning the viewpoint of EM practitioners. Thus, the purpose of this paper is to identify challenges that EM practitioners usually face during their modeling efforts taking into consideration potential influence of these challenges on successful conduct of EM and on alignment of Business and IT thereafter.