Newly introduced scientometric indices have gained much popularity and have been widely discussed. The application of such indices and their validity for Research Performance Evaluation (RPE) focuses on various contexts and aggregate levels. Several methodological concerns have been raised regarding the application of these indices for RPE purpose. This study aims at describing the methodological issues faced and lessons learned from the investigations carried out on engineering research data in Malaysia, using the scientometric approach at meso and micro levels. This scientometric case study employed a set of newly introduced RPE indices along with traditional metrics. The unit of analysis was Malaysian engineering research. At meso level, twelve Malaysian universities were selected. While, at the micro level, a hundred most productive Malaysian related researchers were chosen. The data were retrieved from Web of Science (WoS) for the duration of ten years (2001-2010) and limited to nine WoS engineering categories only. This study enlightens the issues and suggests the possible measures that should be taken into account while conducting the empirical studies by applying scientometric approach to RPE.