One current challenge of magnetic hyperthermia is achieving therapeutic effects with a minimal amount of nanoparticles, for which improved heating abilities are continuously pursued. However, it is demonstrated here that the performance of magnetite nanocubes in a colloidal solution is reduced by 84% when they are densely packed in three-dimensional arrangements similar to those found in cell vesicles after nanoparticle internalization. This result highlights the essential role played by the nanoparticle arrangement in heating performance, uncontrolled in applications. A strategy based on the elaboration of nano-objects able to confine nanocubes in a fixed arrangement is thus considered here to improve the level of control. The obtained specific absorption rate results show that nanoworms and nanospheres with fixed one- and two-dimensional nanocube arrangements, respectively, succeed in reducing the loss of heating power upon agglomeration, suggesting a change in the kind of nano-object to be used in magnetic hyperthermia.