The conversion of a legacy system to a system based on a commercial-off-the-shelf (COTS) package demands a dedicated guidance. The assumption that it is just a matter of adopting a selected package may prove disastrous and even more expensive than building the system in house and from scratch. Building a software solution based on a COTS package not only has its risks, but it is also different from a custom development effort, and it needs to follow a rigorous methodology for a successful implementation. Therefore, it is necessary to define how to solve some of the challenges that this type of project presents, and how to balance customer requirements with the features offered by the COTS package. To successfully and efficiently convert a legacy system into a new system based on COTS package, we developed and present a methodology that utilizes a general process flow chart, simplified Use Cases, and a mapping to the COTS package functionality. We also present the findings of a case study on the applicability and effectiveness of the proposed methodology for the conversion of a legacy Laboratory Information Management System (LIMS).