separate differents fraction to generate specifics serumns

PLEASE HELP!!! hello!! I'm working with a plant extract. I need to separate differents fraction to generate specifics serumns. I want to do size exclution cromatography, but the problem it is the pigments of the plant stain the column. Do you have any idea to remove the pigments previusly or to clean the column? or may be another idea to separate the fractions.