The discovery of an effective and safe pharmaceutical product is based on success in clinical trials. Often, several candidate compounds targeting the same disease area are tested in order to identify the most efficacious products. This involves the manufacture of small quantities of compounds (APIs) for early delivery campaigns. Of these candidates only a few will be successful such that further development is required to scale-up the process. Systematic computer-aided methods and tools are required for faster manufacturing of these API candidates. In this work, a substrate adoption methodology (SAM) for a series of substrates with similar molecular functionality has been developed. The objective is to achieve "flexible, fast and future" pharmaceutical production processes by adapting a generic modular process template. Application of the methodology is illustrated through a case study from the pharmaceutical industry. Use of computer-aided methods and tools as part of the methodology is also highlighted. (C) 2013 Elsevier Ltd. All rights reserved.