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I set up a clearance of 0.256 mm, however, this distance is only applied between the ground and traces. When it comes to ground and pads, this distance is small. I am wondering will be the copper removed from that purple area, between the pads and the ground (see image), and what is the purpose of that purple layer in manufacturing process?

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Look at the Layer Manger on the right. You will see the various layers and their meanings.

I suspect that your purple layer is the F.Mask or front solder mask layer. This will prevent soldermask from being applied over your through hole. There will be copper only where you see the inner gold ring.

If you want to increase the pad clearance, you should click on it and press 'E' for edit. Then look at the "Local Clearance and Settings" tab. There you can override the clearance for a single pad to increase it from the default. You can also set this clearance at the footprint level by choosing the footprint and pressing 'E', then going to the same tab.

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