Traditional ceramic separation membranes, which are fabricated by applying colloidal suspensions of metal hydroxides to porous supports, tend to suffer from pinholes and cracks that seriously affect their quality. Other intrinsic problems for these membranes include dramatic losses of flux when the pore sizes are reduced to enhance selectivity and dead-end pores that make no contribution to filtration. In this work, we propose a new strategy for addressing these problems by constructing a hierarchically structured separation layer on a porous substrate using large titanate nanofibers and smaller boehmite nanofibers. The nanofibers are able to divide large voids into smaller ones without forming dead-end pores and with the minimum reduction of the total void volume. The separation layer of nanofibers has a porosity of over 70% of its volume, whereas the separation layer in conventional ceramic membranes has a porosity below 36% and inevitably includes dead-end pores that make no contribution to the flux. This radical change in membrane texture greatly enhances membrane performance. The resulting membranes were able to filter out 95.3% of 60-nm particles from a 0.01 wt % latex while maintaining a relatively high flux of between 800 and 1000 L/m2·h, under a low driving pressure (20 kPa). Such flow rates are orders of magnitude greater than those of conventional membranes with equal selectivity. Moreover, the flux was stable at approximately 800 L/m2·h with a selectivity of more than 95%, even after six repeated runs of filtration and calcination. Use of different supports, either porous glass or porous alumina, had no substantial effect on the performance of the membranes; thus, it is possible to construct the membranes from a variety of supports without compromising functionality. The Darcy equation satisfactorily describes the correlation between the filtration flux and the structural parameters of the new membranes. The assembly of nanofiber meshes to combine high flux with excellent selectivity is an exciting new direction in membrane fabrication.