We present the possibility of tuning the nanocrystalline microstructure of Co-rich samples by magnetic field annealing. Custom assembly of nucleated grains, aligned in the field direction, has been observed by means of high resolution transmission microscopy. The organized microstructure was obtained on the basis of the appropriate choice of composition, annealing temperature, related to the initial stages of nanocrystallization process, and magnetic field intensity. The linear pattern of the grains has been explained as a consequence of the counterbalance between magnetic, magnetostatic, and magnetocrystalline couplings, only relevant when the nucleation temperature is well below the Curie temperature of the nucleated phase.