Atomic force microscopy and nanoindentation have been applied to the study of thin molecularly templated polymer films. The template was chosen to be the readily hydrogen-bonded cotinine molecule and three different polymer hosts, ElvamideVR nylon, Nylon-6, and poly(4-vinylphenol) were compared. The host polymer was shown to affect the nature of the template-host interaction resulting in varying surface morphologies and differences in the nanohardness. These observations were shown to reflect differences in the underlying interaction chemistry, specifically, whether or not the polymer may be imprinted in the film production process. (C) 2013 Wiley Periodicals, Inc.