This paper considers how to optimize the specification of new built-to-order technology system which takes into user's preference for the system for a manufacturing company. This paper addresses this issue by combining cost-benefit analysis evaluating potential treatment system, and the AHP quantifying subjective judgment in evaluations. A case study is carried out to demonstrate the applicability of the proposed approach. The results show some evidence that the diagnosis procedure succeeded in quantifying user's preference for alternative systems, and that the specification was optimized successfully.