Most of the time rhodamine 6g and methylene blue (these were the only two dyes we had) will stain pdms easily and it will take a reasonable time to de-stain it completely. What we used for the same task was simply a aqueous based ink which is used in ink-pens. Blue, red and black they gave good results without any stain. We checked using Ocean optic spectrometer whether the pdms was stained with these or not. They did not stain it.