In this paper, a three-dimensional multi-criteria mathematical model for class based products is proposed. This model is intended to increase the effective use of space and decrease the material handling cost through allocating items with different sizes and volumes to the most appropriate locations within the warehouse. This model incorporates the realistic constraints normally present in a real-world warehouse planning such as aisle structures, closeness relationships, loading/unloading docks and safety. The proposed model can also be adopted to an FMS environment with automated storage/retrieval system (AS/RS). The capability of the model is shown by applying it to a warehouse layout design for a dynamic food manufacturing and packaging company in Australia. The multiple solutions generated by the model not only reduce the material handling cost significantly but also provide the decision maker with the flexibility to assess the impact of each constraint on the solution generated.