This work reports a new method to hydrophobize glass-based micro- and nanofluidic networks. Conventional methods of hydrophobizing glass surfaces often create particulate debris causing clogging especially in shallow nanochannels or require skilful handling. Our novel method employs oxygen plasma, silicone oil and ultraviolet (UV) light. The contact angle of the modified bare glass surface can reach 100° whilst the inner channels after treatment facilitate stable and durable water-in-oil droplet generation. This modified surface was found to be stable for more than three weeks. The use of UV in principle enables in-channel hydrophobic patterning.