In this paper we present a joint experimental and theoretical approach for the study of the assembly of end-substituted oligothiophenes at surfaces with different polarities (i.e., mica vs graphite). Scanning probe microscopy studies of (sub)monolayer deposits show various types of structures (one-dimensional fibrils, two-dimensional regular layers, and monolayers), depending on the nature of the end groups and the substrate. Using molecular modeling with an atomistic approach, we focus on the interplay between the molecule-molecule (and segment-segment) interactions and the molecule-substrate interactions and their influence on the observed morphologies and the stacking geometry. Such information is relevant for controling the structural order in thin layers of thiophene oligomers for use in field-effect transistor applications, for example, by modifying the nature of dielectric material over which those compounds are deposited.