Achieving precise control of molecular self-assembly to form designed three-dimensional (3D) structures is a major goal in nanoscale science and technology. Using scanning tunnelling microscopy and density functional theory calculations, we show that a 2D covalent organic framework (COF-1) can template solution-processed C60 guest molecules to form several solvent-dependent structural arrangements and morphologies via a 2D to 3D growth process. When 1,2,4-tricholorobenzene is used as solvent, C60 molecules form a template-defined close-packed structure. When heptanoic acid is used as solvent, a range of lower density architectures that deviate from the template-defined close packing are observed. We attribute this difference to the co-adsorption of the heptanoic acid solvent molecules, which is only achieved in the presence of the template. This work demonstrates the possibility to precisely control 3D molecular self-assembly through the synergistic combination of template and solvent effects.