Alignment methods of IC device substrates. A first IC device substrate has a first front side for defining a plurality of first IC features, a first backside opposite the first front side, and a first alignment pattern formed on the first front side or the first backside. A second IC device substrate has a second front side for defining a plurality of second IC features, a second backside opposite the second front side, and a second alignment pattern formed on the second front side or the second backside. A first optical detector and a second optical detector are applied to detect the first and second alignment patterns, so as to align the first and second IC device substrates. Specifically, the first and second alignment patterns face toward the first and second optical detectors in opposite directions.