The invention relates to a method of optimizing an alignment strategy for processing batches of substrates in a lithographic projection apparatus. First, all substrates in a plurality of batches of substrates in the lithographic projection apparatus are sequentially aligned and exposed using a predefined alignment strategy. Then, alignment data is determined for each substrate in the plurality of batches of substrates. Next, at least one substrate in each batch of substrates is selected to render a set of selected substrates including at least one substrate in each batch. In a metrology tool, overlay data for each of the selected substrates is determined. Then, overlay indicator values for a predefined overlay indicator are calculated for the predefined alignment strategy and for other possible alignment strategies. In this calculation, the alignment data and the overlay data of the selected substrates is used. Finally, an optimal alignment strategy is determined, the strategy being defined as alignment strategy among the predefined alignment strategy and the other possible alignment strategies with a lowest overlay indicator value.