Micro-structured array is a crucial optical element with wide range of applications. The optical performance of microstructured array is determined by feature sizes of array, such as diameter, depth and the uniformity across the whole array. Those sizes can be directed retrieved from the 3D profile. We propose a 3D profile measurement system based on light field microscope, which is promising in achieving fast data acquisition by one shot. We propose the principle of measurement, develop the algorithm for focus stack calculation and 3D reconstruction. Preliminary experiments suggest the prospects and challenges.