Femtosecond laser modification of transparent materials offers selective chemical etching, facilitating three-dimensional (3D) micro-structures to open into flexible shapes as configured by multi-line scanning [1] . While surface aberration and other beam shaping methods have been widely studied in processing of transparent glasses [2] , [3] , the influence of such beam shaping on chemical etching has not been addressed. This paper examines the microstructure resulting in fused silica from beams with concave and convex conical phase front [4] . The conical beam shaping is shown to improve etching rates and surface morphology, compensate for deep focussing aberration and provide an attractive tailoring of the microchannel cross-sectional profile.