Block copolymer self-assembly presents a method for pattern and template application on the 10 to 50 nm length scale. However, the research in this area has been limited to the use of only one block copolymer per layer due to the damage and intermixing when spin coating of a second polymer layer. Here we propose a new method that neatly solves the intermixing problem by using a fluorinate photoresist and solvent system. The microdomain orientation within the block copolymer film can be controlled by solvent vapor annealing. And we also observed an improvement of the long-rang order of the microdomains by depositing the block copolymer into lithographical patterned trenches. This orthogonal patterning method allows for the deposition of multiple block copolymers, with ordered microdomains, adjacent to each other on the same layer. The self-assembled patterns can be transferred to the substrate and propose a potential route for the next-generation lithography.