The Femtosecond laser micromachining is a versatile tool for fabrication of microfluidic channel network; we exploit the fast prototyping capability of this technology to produce various channel configurations and study the alignment and topological defects in microchannels filled with Liquid crystals. The configurations consist of multiple intersections of microchannels to form networks both in 2D and 3D. The effect of each configuration on the defect formations is also studied.