We use the "caterpillar" model for accurately calculating the inhomogeneous hydrodynamic friction along a microscopic slender cylindrical filaments using Oseen level hydrodynamics. The methodology is applied to study the motion of a flexible filament in a circularly polarized field. Our results predict that in dilute solution alignment occurs along the axis of the field. For electric fields, the strengths and frequencies required are deduced. These are experimentally accessible. We therefore propose that this is a practical method for aligning filaments such as microtubules and functionalized carbon nanotubes.