Kelvin probe force microscopy (KPFM) is usually applied to map the local surface potential of nanostructured materials at surfaces and interfaces. KPFM is commonly defined as a ‘surface technique’, even if this assumption is not fully justified. However, a quantification of the surface sensitivity of this technique is crucial to explore electrical properties at the nanoscale. Here a versatile 3D model is presented which provides a quantitative explanation of KPFM results, taking into account the vertical structure of the sample. The model is tested on nanostructured films obtained from two relevant semiconducting systems for field-effect transistor and solar cell applications showing different interfacial properties, i.e., poly(3-hexylthiophene) (P3HT) and perylene-bis-dicarboximide (PDI). These findings are especially important since they enable quantitative determination of the local surface potential of conjugated nanostructures, and thereby pave the way towards optimization of the electronic properties of nanoscale architectures for organic electronic applications.