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First you need to define the copper pour outline (if the flooding is done on a routing/outer layers). In this process carefully define the borders of copper pour area. Once this is done the tool will automatically isolate the areas that need not be filled and also create the thermal pads on all those pins which are to be connected to the copper pour. Then do the Copper pour / flood. And you will see that respective pins (which are connected to the pour) will be automatically connected to the pour area. Another thing- make sure to assign the net name GND/VDD to the copper pour area after it's been created.
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