The fabrication of molecular films by coating a conductive polymer solution on a substrate is an active topic in molecular electronics research. Since the inhomogeneity of polymer thin films modulates the chemical states and electrical properties of these films, the construction of integrated polymer devices requires methods to fabricate controllable, homogeneous molecular films as small patterns. Herein, we report the reproducible fabrication of sub-micrometer thickness self-doped polyaniline lines with high homogeneity by fountain-pen lithography (FPL). Compared with commonly used drop-casting and spin-coating methods, the fabrication of line patterns by FPL allows good control of line size, chemical/micro structures, and electronic properties, as demonstrated here by microscope Raman spectroscopy and conductance measurements. Supplying an identical amount of solution from a nanopipette and rapid solvent evaporation are likely crucial for fabricating homogeneous line patterns. This method is promising for the development of molecular electronic devices and the characterization of polymeric materials.