The increasing number of electronic loads has introduced several harmonics into the power system, leading to a growth in the importance of filters intended for their mitigation. Thus, it is important to have the knowledge to select operational limits of each new filter connected in the power grid. Likewise, obtaining these harmonics requires robust tracking systems that provide enough information for better filter selectivity. This paper proposes a selective harmonic active filter control based on Fourier linear combiner (FLC) algorithms for a three-phase electrical grid. The presented system is enabled to track each harmonic order and sequence components with great robustness, extracting positive, negative, and zero sequence information from each harmonic for further filter selectivity. It also proposes a new strategy to improve the FLC-based algorithms in tracking frequencies in power grid disturbances. Simulated results of the algorithm and a real-time simulation of a selective active power filter (SAPF) were presented, validating the performance in several scenarios.