In order to control the length of micro-channels ablated at the surface of dielectrics, we use annular filtering apertures for tailoring the depth of focus of micrometric Gaussian-Bessel beams. We identify experimentally and numerically the appropriate beam truncation that promotes a smooth axial distribution of intensity with a small elongation, suitable for processing micro-channels of small aspect ratio. Single-shot channel fabrication is demonstrated on the front surface of a fused silica sample, with sub-micron diameter, high-quality opening, and depth of few micrometers, using 1 ps low-energy (< 0.45 µJ) pulse. Finally, we realize 10 × 10 matrices of densely packed channels with aspect ratio ~5 and a spatial period down to 1.5 μm, as a prospective demonstration of direct laser fabrication of 2D photonic-crystal structures.