Low-temperature plasma treatments are used to perform surface modification on polymers, aiming to improve the surface properties according to the desired application. In this work, polyelectrolyte multilayers (PEMs), built by layer-by-layer deposition technique, were treated using high frequency low-temperature air plasma. We evaluated the effect of the exposure time (20 and 300 s) and its effects on PEMs with two different top layers: alginate and carboxymethylcellulose. Chitosan was used as the cationic polymer to build the LbL films with the oppositely charged anionic polymers, alginate and carboxymethylcellulose. Our results showed that the surface topology, wettability and free charges within layers are highly correlated to the polymer pair used. PEMs of the chitosan/alginate system are thinner and hydrophilic, and present a surface with wider peaks. 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