We present an improved method to prepare carboxylic acid (COOH) and amine (NH2) terminated self-assembled monolayers (SAMs) of alkanethiolates. In this method, a small amount of CF3COOH (for COOH-SAM) or N(CH2CH3)3 (for NH2-SAM) is added into the ethanolic solution of alkanethiols during SAM formation. The freshly formed COOH- and NH2-SAMs are then rinsed with an ethanolic solution of NH4OH or CH3COOH, respectively. Both SAMs prepared with the improved method show better quality in terms of surface chemical composition, roughness, and wettability as measured by X-ray photoelectron spectroscopy, atomic force microscopy, and contact angle, respectively. The formation of better SAMs can be attributed to the disruption of interplane hydrogen bonds.