Do mean for looks or to improve cooling? I wouldn't try to smooth the bottom of a sink or waterblock with a dremel, you'll have to lap that.
There are more detailed descriptions available, but basically you get a pane of glass and some very fine sand paper (400-200 grit). Then flatten the paper on the glass and slowly drag the sink along it. I've had mixed results doing it. On an Alpha, it actually made it a little worse. On old sinks I pulled from dumpstered machines, it improved them a good deal.
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