Methods for aligning layers more accurately for FinFETs fabrication. An embodiment of the method, comprises: forming a plurality of dummy line features and a plurality of spacer elements according to a first pattern; removing portions of the plurality of spacer elements and portions of the plurality of dummy line features according to a second pattern; defining a reference area by removing some unwanted spacer elements according to a third pattern; aligning a front-end-of-line (FEOL) layer in X direction with the reference area defined by the third pattern; and aligning the FEOL layer in Y direction with the plurality of spacer elements defined by the first pattern. The reference area may be an active area or an alignment mask. The plurality of dummy line features and the plurality of spacer elements are formed on a substrate. The FEOL layer may be a poly layer or a shield layer.