This communication provides a facile method for distributing and dispersing molecules within a molecular template. Using the self-assembled template of oligo(phenylene-ethynylene) (OPE), organic molecules such as coronene (COR) and biomolecules such as tripeptide are controllably distributed and dispersed within this molecular template on highly oriented pyrolytic graphite (HOPG) surfaces. COR molecules were controllably distributed into various regular arrays by simply adjusting the molecular molar ratio, while tripeptide molecules were uniformly positioned at the vacancies of the OPE template.