adobe photoshop - Remove (or mask) a specific colour from multiple layers CS5

This question seems to have been asked a number of times but either the requirements are different or I'm not able to follow the answers.

I have an animated GIF that was created using a third party tool. This tool uses solid green (#00ff00) as the colour to represent transparency.

This GIF needs editing as it needs breaking down into different sections to produce multiple smaller GIFs, I'm doing this in Photoshop CS5.

However I can't seem to replace the green with transparency, when I export the GIF from CS5 the green is there as a solid colour.

So what Im asking is:

1. 
   

   Is there anyway to tell the "Save to Web" tool that #00ff00 should be transparent, OR

   
   



2. 
   

   How can I delete the colour from all of the layers (there are 591 of them), OR

   
   


3. 
   

   Is there anyway I can use a mask to make that colour transparent?

   
   

Answer

When saving as a GIF using Save for Web you can select any number of colors in the color table and click the button to the far left below the table to map those colors to transparency: