In this paper, the effect of the capillary structure and its organization in a multicapillary electrophoresis system (MES) were studied. The model was based on a combination of the dynamics of energy transport and the mathematics of fractal geometry. It demonstrated that in order to minimize the energy transport the geometric system structure must obey certain power laws. The results obtained showed that these power laws depend on the hydrodynamic regime and the capillary material. For polymeric capillaries in a pulsed flow, the viscous resistance in the fractal multicapillary system (FMS) varied with 1/r(2) for the smallest capillaries (r was the dimension of the capillary cross-section) and with 1/r(4) (Poiseuille flow regime) for the largest capillaries. For a constant flow, the Poiseuille regime was always respected. The FMS can use high field strengths without too much energy dissipation to perform rapid and efficient separation.