Harmonic current estimation is the key aspect of Active Power Filter (APF) control algorithms to generate a reference current for harmonic compensation. This paper proposes a novel structure for harmonic current estimation scheme based on Trigonometric Orthogonal Principle (TOP) and Self Tuning Filter (STF). The key advantages of the proposed method are its simplicity, low computational burden and faster execution time in comparison to the conventional harmonic current estimation approaches. The TOP method provides a simple and fast approach to extract the reference current, while STF provides a simplified structure to generate the required synchronization signal that eliminates the need of a Phase Locked Loop (PLL) algorithm for synchronization. As a result, it exhibits less complexity in implementation and less consumption of microcontroller`s resources; thus, the proposed method can be implemented using a low-cost microcontroller. It is shown in the paper that the proposed method provides 10 times gain in processing speed as compared to the conventional DQ method. The proposed approach is analyzed in detail, and its effectiveness and superior performance are verified using simulation and experimental results.