Segmentation can degrade a high-quality dose distribution obtained by fluence map optimisation (FMO). A novel algorithm is proposed for generation of MLC segments to deliver an FMO plan with step-and-shoot IMRT while minimising quality loss. All beams are considered simultaneously while generating MLC segments for reproducing the 3D FMO dose distribution. Segment generation is only steered by the 3D FMO dose distribution, i.e. underlying FMO fluence profiles are not considered. The algorithm features prioritised generation of segments, focusing on accurate reproduction of clinical objectives with the highest priorities. The performance of the segmentation algorithm was evaluated for 20 prostate patients, 15 head-and-neck patients, and 12 liver patients. FMO dose distributions were generated by automated multi-criteria treatment planning (Pareto-optimal plans) and subsequently segmented using the proposed method. Various segmentation strategies were investigated regarding prioritisation of objectives and limitation of the number of segments. Segmented plans were dosimetrically similar to FMO plans and for all patients a clinically acceptable segmented plan could be generated. Substantial differences between FMO and segmented fluence profiles were observed. Avoidance of the usual reconstruction of 2D FMO fluence profiles for segment generation, and instead simultaneously generating segments for all beams to directly reproduce the 3D FMO dose distribution is a likely explanation for the obtained results. For the strategies of limiting the number of segments large reductions in number of segments were observed with minimal impact on plan quality.