The solution-based fabrication of organic polymer thin film is essential for molecular functional devices. Although there are numerous techniques to cast such thin films, the qualitative variation in the film is still a big issue. Herein, the reproducible fabrication of nano-thickness self-doped polyaniline (SPAN) thin films with high uniformity by fountain-pen lithography (FPL) is reported. Compared to commonly used drop-casting and spin-coating method, it is conformed that the films fabricated by FPL provides a high controllability of film size, chemical/micro structures and electronic properties, which is characterized by microscope Raman spectroscopy and current-voltage (I-V) measurement. Such method is potentially a reliable choice for the development of molecular electronic devices and the characterization of polymeric materials.