Noisy fluorescent gels - (Nov/29/2010 )

Hi all. I am using a Typhoon Imager (532 nm excitation, 580 bp 30 emission filter) to detect some small fluorescent compounds (Cy3 derivatives) in a 12% PAGE minigel (8 x 8 cm). I think I can detect the compounds, but I am not satisfied with my reproducibility. There seem to be fluorescent contaminants on the gel that give a high background signal. I try to clean off the gels with a kimwipe and water, but the images remain noisy. Any ideas about keeping PAGE gels clean and reducing fluorescence background?
Thanks!

need more information.

is the gel fixed? if so, with what?

stained with anything else (eg coomassie)?

in what is the gel stored?