This work is based on the management of fuel waste from Spanish nuclear power plants. It is planned to activate individualized temporary warehouses (ITW) when the saturation of the pool intended to hold spent nuclear fuel elements is reached while the facility is operated. At the end of this period, an ITW can be used as a short or long-term temporary warehouse until the central temporary warehouse (CTW) is available. The fuel/combustible elements (EC), spent and located in the nuclear power plant (NPP) pool, are selected for storage in containers (capsules). There exist a series of restrictions imposed on each ITW by the competent regulatory organism in function of the requirements that specifically affect the containers (e.g. a limit of the thermal load or the number of positions for fuel elements). The characteristics of these capsules determine the minimum cooling time of the fuel in the pool of the nuclear power plant and, consequently, the time necessary to completely empty the pool. In this context, we present a Mixed Integer Linear Programming model with the aim of minimizing the cost of MPC (Multi-Purpose Canister) capsules necessary to relocate in an ITW the maximum number of spent fuel elements available in the pool in a pre-established date. This must be done in a single load. We also propose an exact algorithm (A1) that, based on a MILP-1 solution, is capable of assigning fuel elements to capsules with two regions limited in decay heat. The proposed method (MILP-1 plus A1) can solve instances with 1500 fuel elements, 6 types of regions and 4 types of containers in a CPU time of less than 0.75 seconds.