Precise three dimensional (3D) profile measurements of vertical sidewalls of concave micro-structures are impossible by conventional profiling techniques. This paper introduces a simple technique which can obtain 3D sidewall geometry by means of laser fluorescent confocal microscopy and an intensity gradient algorithm. The measurement principle is: when a concave micro-structure is filled up with fluorescent solution, the position where the maximum intensity variation lays represents the profile of the micro-structure in the fluorescent 3D volume image. The physical essence behind this measurement principle is analyzed in this paper in detail. The strengths and limitations of this technique are studied by experiments or by illustrations. The factors that are able to improve the measurement accuracy are discussed. This technique has demonstrated the capability for measuring of 3D geometry of various concave features, such as vertical, buried and other micro channels with sub-mum (RMS) measurement accuracy and repeatability.