This paper proposes a study on the development of automated custom software that uses the targeted functional analysis (TFA) methodology, in order to provide solutions for the optimal concept of bespoke medical products obtained with additive manufacturing (AM) technologies. The software, Custom-Med, provides a friendly Lab View interface and is easily adaptable for any single part medical product. The functional analysis uses tools like FAST diagrams, product life cycle analysis, technical and economic matrices. The study focuses on the functionality of the product throughout its life cycle, starting with development, production, usage, maintenance and finishing with storage or disposal. These become key input parameters when running Custom-Med. The main advantages brought by deploying a custom software application tool that uses the TFA methodology are: accurate technical parts, high quality, and customization for AM applications and reduced time for product development. Custom-Med is tested for validation purposes on three distinct medical products which are: a mandibular surgical guide, an adaptive ophthalmic speculum and vacuum surgical device. All three products are used for intraoperative surgical procedures.