We describe an accurate method to measure velocity profiles in thin microchannels, using particle image velocimetry combined with a nano- positioning system. The experimental setup is used to measure the slip length for water flowing along an hydrophilic surface, pyrex glass, and an hydrophobic one, a monolayer of octadecyltrichlorosilane on silicon. This method has a few percent precision on the velocity, 100nm-accuracy on the determination of the wall position, and a similar precision for the position of the fluid layer where the measurement is performed. . These characteristics allow to determine, with unprecedented accuracy (?100nm), slip lengths for water flows over glass; this represents a substantial improvement (a factor of 6 or so) compared to previous work using a direct method. When applied to glass surfaces, one gets slip lengths equal to 0?100nm. For functionalized silicon surfaces, the accuracy is lower. One obtains 200?300nm in this particular case.