how can a microscopic filter seperate molecules by shape?

Some molecules are "long," while others are more "round." Take ortho- and para xylenes. The ortho- isomer is a hexagonal benzene ring with two methyl groups next to one another. This is a round molecule. The para-isomer has the methyl groups on opposite corners of the hexagon. Thus they extend the length of the molecule. If you had a zeolite mineral filter, then the para-xylene might seem longer and thinner, and it might fit into a cavity in the mineral and be trapped there. The squatter ortho- molecule might not be absorbed, because it doesn't fit.