I'm not sure what you mean by "top and bottom." If it's during import, select the "bottom" button to get a uniform blue color on the model (that moves the model down to be fully inside your block of wood). Darker blue areas indicate to model is being sliced and not completely inside the material. Then click OK.
Since you only have post a few times, I'm guessing you're new to VCP. In the 2D view, select all. You should be able to then re-size with the corner squares to get a 90mm dish.
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