This paper presents an evaluation of efficiency on glass precision machining by using abrasive water-jet machine. In this study, problems of conventional water-jet machining are examined experimentally and are analysized numerically. Especially, the reason of whitening on the machined surface of biochip glass is determined. It is found that the mass flow rate of abrasive input and transverse speed of water-jet are key parameters to control the direct machining of micro hole and channel on a glass substrate. Based on results of experimental analysis, possibility of direct fabrication of micro holes and channels on a glass substrate is successfully confirmed.