How can I get my convertible top clean?

I have a 98 eclipse spyder with a vinyl khaki top and it has like darkened spots on it from what appears where rain water sits or runs over a lot. I guess its mildew. I have bought blue magic top cleaner but it won't get rid of the spots. When I look real close and take my nail i can get it down in between the little grooves and sc the black stuff off. I guess the cloth isn't fine enough to get down in there and loosen it up. What can I use to get rid of these spots? Like a soft bristle brush or something?