In Ayurveda medicine, correct identification of medicinal plants is of great importance. Plants are identified by human experts using their visual features and aroma. Incorrect identification of medicinal plants may lead to adverse results. Plant identification can be automated using visual morphological characteristics such as the shape, color, and texture of the leaves and flowers. This paper presents how rare medicinal plants were identified with high accuracy by applying image processing and machine learning capabilities. For this study, a database was created from scanned images of leaves and flowers of rare medicinal plants used in Sri Lankan Ayurveda medicine. Both the front and back sides of leaves and flowers were captured. The leaves are classified based on the unique feature combination. Identification rates up to 98% have been obtained when tested over 10 plants.