In capillary electrophoresis, effective optical signal quality improvement is obtained when high frequency (>100 Hz) external pulse fields modulate analyte velocities with synchronous lock-in detection. However, the pulse frequency is constrained under a critical value corresponding to the time required for the bulk viscous flow, which arises due to viscous momentum diffusion from the electro-osmotic slip in the Debye layer, to reach steady-state. By solving the momentum diffusion equation for transient bulk flow in the micro-channel, we show that this set-in time to steady-state and hence, the upper limit for the pulse frequency is dependent on the characteristic diffusion length scale and therefore the channel geometry; for cylindrical capillaries, the set-in time is approximately one half of that for rectangular slot channels. From our estimation of the set-in time and hence the upper frequency modulation limit, we propose that the half width of planar channels does not exceed 100 microm and that the radii of cylindrical channels be limited to 140 microm such that there is a finite working bandwidth range above 100 Hz and below the upper limit in order for flicker noise to be effectively suppressed.