Most multiple sequence alignment programs use heuristics that sometimes introduce errors into the alignment. The most commonly used methods to correct these errors use iterative techniques to maximize an objective function. We present here an alternative, knowledge-based approach that combines a number of recently developed methods into a two-step refinement process. The alignment is divided horizontally and vertically to form a lattice in which well aligned regions can be differentiated. Alignment correction is then restricted to the less reliable regions, leading to a more reliable and efficient refinement strategy.