I often run into this issue. I'm creating a file in Photoshop with masked layers etc. I want to make the final output available for some mock-ups in Illustrator, so I rasterize the layers and marquee select the entire area, copy and move to Illustrator.
Pasting the area in Illustrator flattens all transparencies, which is quite annoying. I'm left with my object and a flat white background.
Is there a reason for this?
Answer
I'm not sure why you're rasterizing the layers, nor why you would want to copy and paste rather than place the image in AI. If there isn't a vital reason for that workflow, Place the PSD in Illustrator (File > Place) instead. All of the transparency is preserved, layers are intact.
Once the image is placed, you can embed it if necessary. One of the embed options is to flatten all layers, which also preserves transparency. If you don't flatten, "Convert Layers to Objects" opens up various possibilities for subsequent editing.
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