We show that uniform nanoripples can be produced on the sidewalls of the micro-cell vertically embedded in fused silica glass by femtosecond laser direct ablation. The nanoripples can be used for homogeneous liquid crystal (LC) alignment with different azimuthal angles. The azimuthal anchoring energy at the interface between the LC and nanoripples is obtained by measuring the twist angle of LC director in the fabricated twisted nematic LC micro-cell. This method allows for fabrication of LC micro-cells integrated in glass chip with three-dimensional (3D) configurations, opening a new venue to fabrication of 3D miniaturized LC devices. (C) 2010 Elsevier B. V. All rights reserved.