I created a large component.  The pads are 2mm hole with a solder mask of 2mm. The copper fill is going right up to the solder mask. Example, Create a pad with a 1mm hole, and a solder mask of 0.5mm. Then do a fill with a clearance of 0.5mm. Notice it did not keep 0.5mm clearance around the pads' solder mask. This appears the copper fill tool does not take into account the solder mask size when calculating clearances. Or am I doing this wrong?