Depending on what molecules are you talking about? If you are referring to proteins then it is possible to develop nanostructures ( i.e. nanowires, nanotubes, nanorings and nanofibers) that are selective towards a specific protein. Designing nanostructures bound with a self assembled monolayer (SAM), that is functionalized with an antibody specific to an protein of interest, could be used to selectively isolate a protein. Functionalized nanostructures would preferably be on a solid surface as the isolation of free nanostructures from solution might be difficult. One might try and assess whether the compound (i.e. Si, ZnO, Ag, Au and C) used for nanostructure growth has a unique characteristic which could be harnessed to assist in the isolation of the nanostructures, however, while keeping the protein of interest functional.
Researchers have developed an nanowire based protein isolation devices on solid surfaces. Have a look at the following article.
1) V Krivitsky Affiliation: School of Chemistry, the Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel.; LC Hsiung; A Lichtenstein; B Brudnik; R Kantaev (2012). Si nanowires forest-based on-chip biomolecular filtering, separation and preconcentration devices: nanowires do it all. Nano letters, 12(9) 4748-56.