kicadpcb
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?
Yes, this is done in the DRC settings. One of the parameters sets how far traces must be from board edges, which includes the edges of unconnected holes. I don't remember the exact setting name, but run "drc", look thru the settings, and you should be able to spot it.
You are saying you looked in the DRC but didn't find it. It's actually quite obvious and one of only two setting under the "Distance" tab:
You don't really need to tell KiCad that the pins are connected elsewhere. DRC and ERC errors will not prevent the program from producing Gerber files - they are just warnings to you that something doesn't comply with the rules you have given to program.
It is safe to ignore DRC and ERC errors, providing you know why the errors are there, and are certain that they are acceptable. It is, of course, best if you can clear all errors, but occasionally some errors are unavoidable (or it is too hard to adjust the rules to avoid the errors).
Best Answer
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.