Formation of fluidic channels with well-defined size and shape is of critical importance for reliable resistive pulse sensing of individual objects in electrolyte solution. Here we report on a method to fabricate a pore of 3D-controlled structure. We directly sculpted a hole in a polymer resist membrane of various thickness up to 6 µm by electron beam lithography. This procedure allowed to create diverse range of thickness-to-diameter aspect ratio channels of controllable shapes from concave to convex cone profiles via the varying proximity effects under different electron dose conditions. The lithographically-defined pores were utilized to detect nanoparticles by cross-membrane ionic current that revealed optimal membrane thickness for gaining larger resistive pulse signal intensities. The present technique provides a way to design single-particle sensors for cell sorting and viral screening.