Segmentation of the iris is a crucial stage in an automated iris-based recognition system. The performance of any biometric system primarily relies on how effectively the iris is extracted from the unwanted parts of an iris image. The process of iris segmentation is mainly affected by the noise artefacts such as eyelid/eyelashes occlusions, specular reflections, intensity inhomogeneities, and non-circularity of the iris boundary. A novel and an efficient method has been proposed in this work to segment noisy and non-circular iris boundaries. The mathematical modelling of morphological reconstruct fuzzy C-means clustering (MRFCM) has been presented. The MRFCM based on improved particle swarm optimisation has been implemented before the segmentation in the recognition framework. The resultant images are then segmented by employing geodesic active contours incorporated by a new stopping function. The effect of the proposed segmentation method on iris recognition is observed through matching score distribution. The popular and publicly available datasets such as UBIRISv1, CASIA-v3-Interval, MMU1, and Mobile Iris Challenge Evaluation databases are considered for the evaluation of the proposed method. Recognition accuracy is validated and compared with the well-existing methods.