We demonstrate the use of molecular recognition to control the spatial distribution of guest molecules within block copolymer films. Block copolymers bearing recognition units were combined with complementary and noncomplementary molecules, and the extent of segregation of these molecules into the different domain types within microphase-separated thin films was quantitatively analyzed using dynamic secondary ion mass spectrometry (SIMS). Complementarity between the guest molecules and the polymer functionalities proved to be a key factor and an efficient tool for directing the segregation preference of the molecules to the different domain types. The effect of segregation preference on the glass transition temperature was studied using differential scanning calorimetry (DSC), and the results corroborate the SIMS findings. In a complementary study, guests with tunable sizes (via dendron substituents) were used to control block copolymer morphology. Morphological characterization using transmission electron microscopy (TEM) and X-ray diffraction reveal that selectivity differences can be directly translated into the ability to obtain different morphologies from recognition unit-functionalized block copolymer scaffolds.