Very creative! I think polymer clay is perfect for crafting your own custom sized eyes for small plushies, if the safety eyes dont fit or you dont like the look of it. You only have to bake it for a few minutes if the bead is small! Embroidery is also feasible and pretty on miniatures.
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My last finished (self-designed) amigurumi was a cat and it was really difficult to make eyes that look like I wanted them to be. The best solution I came up with was to use cotton fabric from an old T-shirt, which I painted with acrylic pens. I glued them to the actual amigurumi and then embroidered kind of an eyelid around the eye. Im very proud of them!