Fabricating ultrathin organic semiconductor nanostructures attracts wide attention towards integrated electronic and optoelectronic applications. However, the fabrication of ultrathin organic nanostructures with precise alignment, tunable morphology and high crystallinity for device integration remains challenging. Herein, an assembly technique for fabricating ultrathin organic single-crystal arrays with different sizes and shapes is achieved by confining the crystallization process in a sub-hundred nanometer space. The confined crystallization is realized by controlling the deformation of the elastic topographical templates with tunable applied pressures, which produces organic nanostructures with ordered crystallographic orientation and controllable thickness from less than 10 nm to ca. 1 μm. The generality is verified for patterning various typical solution-processable materials with long-range order and pure orientation, including organic small molecules, polymers, metal-halide perovskites and nanoparticles. It is anticipated that this technique with controlling the crystallization kinetics by the governable confined space could facilitate the electronic integration of organic semiconductors.