This study presents a thorough discussion of the efficiency and effectiveness improvement from optimization models (Binary Linear Programming and Goal Programming), as applied to the Department of Defense’s Readiness and Environmental Protection Initiative. The OM models can yield 21% and 19.1% higher benefit scores respectively, spending $13,013,473 and $31,463,473 less total acquisition costs. To achieve the same level of conservation benefits for the current rank based approach, the REPI would spend additional $20.1 million and approximate 50% of the budget. A counterpart of OM- the cost-effective analysis is observed to be inefficient when the problem becomes complex. In a real world of political environment of the conservation programs, we suggest a hybrid method of current rank based approach and the OM as well as the GP to address incompatible goals of interests groups.