Bumps are important structures for electrical interconnection and structural support between die-to-die and die-to-wafer interfaces in advanced packaging. Their height and coplanarity affect electrical performance and heat dissipation. In this study, a microscopic fringe projection profilometry (MFPP) measurement system is built and calibrated with high precision. Then, the proposed multi-exposure method based on intensity modulation threshold segmentation is compared with two existing methods. Highly reflective areas at bump tops are effectively measured, thereby facilitating three-dimensional bump data measurement. Thereafter, an automatic method of calculating the bump height and planarity based on K-means clustering segmentation is proposed. Experiments are conducted to verify the measurement accuracy of the system. The calculated bump heights in this paper are compared with those measured using a white-light interferometer. The results demonstrate that the proposed method achieves micron-level topography measurement of highly reflective bumps.