FoldMason is a C++ command-line tool for constructing accurate multiple sequence alignments (MSAs) from large sets of protein 3D structures. It uses Foldseek's 3Di structural alphabet and a progressive alignment scheme guided by a structure-derived tree. FoldMason scales to tens of thousands of structures, optionally pre-clusters input structures, supports iterative refinement, and can compute Local Distance Difference Test (LDDT) scores over the MSA columns to quantify structural alignment quality.