Self-mixing interferometry (SMI) is considered both efficient and accurate for alpha factor measurement. In this work, a high-performance filtering method and effective data processing algorithms are combined to optimise the measurement accuracy on the frequency-domain based alpha measurement method. In order to achieve fast real-time measurement, FPGA (Field Programmable Gate Arrays) is employed for the implementation of the proposed algorithms. The FPGA design includes noise reduction, SMI signal normalisation, phase signal detection, spectrum calculation and alpha estimation. The results show that the FPGA based design can achieve fast and reliable alpha factor measurement.