I've created a (very) large image in illustrator, a portion of which is shown. There are numerous circles on top of each other with their transparencies set to multiply (so that Yellow over Cyan produces Green - similar to a color halftone effect). I've used pathfinder to divide all the shapes (and ungrouped). I would now like to select all the visibly different color shapes and place on different layers (so C, M, Y, K, C+M, C+Y, M+Y, etc). When I go to Select>Same>Appearance or Fill, I am only able to select the base color (C,M,Y or K), not the Greens (C+Y) or Reds or Purples. Is there any way to 'combine' the C+Y (etc) so it becomes a single color to select? (Or another way to achieve the same effect?) Obviously, I could manually select individual objects, but the size of the image actually makes this next to impossible. TIA!
Select all your shapes and go to Object> Flatten Transparency. This will "bake in" the blend mode color so that you can then select these shapes with Select> Same Fill Color. This will group everything so you can un-group if desired (Object> Ungroup).
This will leave the underneath shape intact but will divide the upper shape (the one that had the blend mode applied) into 2 separate shapes- so the Pathfinder divide step would be unnecessary.
The down side to this is that you would not be able to move things around afterward so I would suggest copying all your shapes before you do this to a new locked layer so you can access them again if needed or save an extra copy of the document prior to flattening.
Perhaps you should check Layers panel, because "Select same .." doesn't work if the whole layer is highlighted. In order to work properly, object should be highlighted as well as selected. That is that blue highlight in Layers panel. Those are two separate things. So, select object, and make sure it's also highlighted in Layers panel, and then go to Select same appearance.