With the development of combinatorial materials research (CMR) methods and high throughput experimentation (HTE) workflows for polymer research applications, the demand for automated, high throughput characterization methods is evident. Solution-based characterization methods like NMR, GPC, viscosimetry, for example and UV-Vis as well as fluorescence plate readers are available. Here we report on the incorporation of automated scanning probe microscopy in the HTE-workflow by demonstrating the evaluation of surface properties and topographies for thin polymer film libraries.