: New approaches to modeling and design of enterprise systems must enable enterprises to offer dramatically improved capabilities including more effective enterprise architectures, more efficient business processes, the ability to engage in new much more dynamic forms of global co-operation, and greatly improved interoperability. The focus of the work in this paper is the application of agent-oriented software development methodologies to architecture enterprise modeling as well as the management of the variability guided by a strategic cost/schedule/quality or benefit/value/risk goals. This study will be the first step of working towards enabling tool support for enterprise variability management, enterprise modeling, validating and deducting the consequences of constrains or feature interactions in enterprise organization.