We propose a windowed Fourier-filtered and quality-guided phase-unwrapping algorithm that is an extension and improvement of our previous phase-unwrapping algorithm based on windowed Fourier transform [ Opt. Laser Technol. 37, 458 (2005), Key Eng. Mater. 326–328, 67 (2006)]. First, the filtered amplitude is used as a real-valued quality map, rather than a binary mask, which makes the phase- unwrapping algorithm more tolerant to low-quality regions in a wrapped-phase map, and the process is more automatic. Second, the window size selection is considered, which enables the algorithm to be adapted to tackle different phase-unwrapping problems. A large window size is useful for removing noise, building long barriers along phase discontinuities, and identifying invalid regions, while a small window size is useful for preserving local features, such as small regions and high-quality narrow channels. Eight typical examples in Ghiglia and Pritt’s excellent book Two-Dimensional Phase Unwrapping: Theory, Algorithm and Software (Wiley, 1998) are used to evaluate the proposed algorithm. The proposed algorithm is able to unwrap all these examples successfully. The windowed Fourier ridges algorithm, another algorithm based on windowed Fourier transform, is also tested and found to be useful in building barriers along phase discontinuities.