The use of low-energy femtosecond laser beam combined with chemical etching has been proven to be an efficient method to fabricate three-dimensional structures in fused silica. For high-volume application, this technology – like other serial processes – suffers from a moderate production rate. Here, we show that femtosecond laser can also be employed to fabricate silica molds and other patterned surfaces, including surfaces with high aspect ratio features (> 10). Through appropriate tailoring of silica’s surface property and subsequent creation of, for instance, simple elastomeric molding, new opportunities for the indirect 3D, multi-scale spatial characterization of deep laser-fabricated microstructures come along. We demonstrate that those moldings are characterized by a high fidelity (down to the nanometer scale) to the silica mold. These results further advance the applicability of femtosecond laser processing to glass.