We demonstrate the spatial separation of the cis- and trans-conformers of 3-fluorophenol in the gas phase based on their distinct electric dipole moments. For both conformers we create very polar samples of their lowest-energy rotational quantum states. A >95% pure beam of trans-3-fluorophenol and a >90% pure beam of the lowest-energy rotational states of the less polar cis-3-fluorophenol were obtained for helium and neon supersonic expansions, respectively. This is the first demonstration of the spatial separation of the lowest-energy rotational states of the least polar conformer, which is necessary for strong alignment and orientation of all individual conformers.