A method for manufacturing a microfluidic device (100) includes depositing a bonding layer (106) on a surface of a second glass layer (104a) of a glass substrate having a first glass layer (102) and the second glass layer (104a) fused to the first glass layer (102), such that a masked region of the surface is covered by the bonding layer, and an exposed region of the surface is uncovered by the bonding layer; removing a portion of the second glass layer corresponding to the exposed region of the surface to form a flow channel (112) in the glass substrate; and bonding a cover (108) to the glass substrate with the bonding layer (106).