We have shown that control of stochastic multiple filamentation may be performed with either large - scale spatial modifications of the beam, such as squeezing the whole beam, or relatively small-scale periodic light field perturbations introduced into the transverse beam distribution. We have found that the average conversion efficiency to the supercontinuum grows according to the similar law in both small beam and large beam cases, starting from the point of the parent filament formation. Stability of the supercontinuum signal grows essentially with decreasing initial beam size. Periodic intensity and phase perturbations are used to control stochastic filamentation arising in atmospheric turbulence. Regular phase fluctuations are introduced into the beam in the form of a lens array. With decreasing array period the spatial arrangement is attained earlier in the propagation distance. In addition, the amplitude of multiple filaments has smaller fluctuations relatively to the propagation in the regular medium. In the case of periodic intensity perturbations, control of stochastic filaments is more pronounced as compared with the phase perturbations of the same period. However, introduction of amplitude perturbations leads to the energy loss from the initial pulse.