We present the design of an automated spin-coater that facilitates fabrication of polymer films based on molecular layer-by-layer (mLbL) assembly. Specifically, we demonstrate the synthesis of ultrathin crosslinked fully-aromatic polyamide (PA) films that are chemically identical to polymer membranes used in water desalination applications as measured by X-ray photoelectron spectroscopy. X-ray reflectivity measurements indicate that the automated mLbL assembly creates films with a constant film growth rate and minimal roughness compared with the traditional interfacial polymerization of PA. This automated spin-coater improves the scalability and sample-to-sample consistency by reducing human involvement in the mLbL assembly.