The invention relates to methods and apparatus in which a plurality of ALD reactors are placed in a pattern in relation to each other, each ALD reactor being configured to receive a batch of substrates for ALD processing, and each ALD reactor comprising a reaction chamber accessible from the top. A plurality of loading sequences is performed with a loading robot. Each loading sequence comprises picking up a substrate holder carrying a batch of substrates in a storage area or shelf, and moving said substrate holder with said batch of substrates into the reaction chamber of the ALD reactor in question.