Understanding the principles of molecular recognition is a difficult task and calls for investigation of appropriate model systems. Using the manipulation capabilities of scanning tunneling microscopy (STM) we analyzed the chiral recognition in self-assembled dimers of helical hydrocarbons at the single molecule level. After manual separation of the two molecules of a dimer with a molecule-terminated STM tip on a Cu(111) surface, their handedness was subsequently determined with a metal atom-terminated tip. We find that these molecules strongly prefer to form heterochiral pairs. Our study shows that single molecule manipulation is a valuable tool to understand intermolecular recognition at surfaces.