Interaction between molecules and surfaces and nucleation processes during organic thin film growth have been studied by modulated molecular beam experiments. After a brief introduction of the background and the experimental technique, we describe the results of our study on the interaction between pentacene and chemically modified SiO₂ surfaces. Molecular migration on regularlly-stepped vicinal surfaces of silicon and crystal nucleation controlled by pulsed supply of the molecules are discussed on the basis of the experimental data on phthalocyanine and quinacridone.