The sample solvent in GPC should normally dissolve the entire sample, negating the need for the column to be cleaned. However if it is evident that the column is contaminated, the first consideration is what component of the sample is likely to be sticking. Once the source of contamination has been identified, a solvent which is suitable for dissolving it should be selected.
Note that it is important to consider whether the solvent chosen is miscible with the current mobile phase, and also what degree of swell the two different solvents impart on the packing material. Provided there is not a large difference in swell, and the two solvents are miscible, the column can then be flushed with the cleaning solvent for 20 column volumes, before returning to the method mobile phase.