I suggest that you follow this feed on Quora: https://www.quora.com/How-do-I-measure-clearly-the-thickness-of-a-thin-film-using-AFM
In addition, check out the following paper by Üzüm et al., "Growth behaviour and mechanical properties of PLL/HA multilayer films studied by AFM", 2012 - http://www.beilstein-journals.org/bjnano/articles/2190-4286-3-87