Subtract Shapes is used to subtract one shape from another resulting in a single merged shape.

Merge Shapes is used to combine two or more shapes (copper planes or copper plane cutouts) into a single merged shape. 

How to turn all 2D lines into keepout together 

==================================================

Subtract Shapes is used to subtract one shape from another resulting in a single merged shape. This is not restricted to copper plane cutout shapes; a copper plane shape can be subtracted from another copper plane shape.

1. A shape subtracted from another shape that completely severs the first shape results in two separate shapes.
2. A shape completely within a plane which is subtracted is treated as a void and combined with the plane so that it moves with the plane (unlike a cutout which tracks separately). Subtracting the shape may not be the best choice in this case and it may be better to keep it as a cutout so the void shape can be more easily moved or copied. The copper plane will have an opening in the flooded shape either way.

Tip: Make sure that you are in Pour Outline mode when attempting to merge or subtract shapes. Use the modeless command PO and press Enter to toggle the setting.

Merge Shapes is used to combine two or more shapes (copper planes or copper plane cutouts) into a single merged shape. Each location where a shape intersects another shape results in a single shape that expands to include the additional shapes.

1. You must select two (or more) shapes before merging shapes.

 2. The shapes need to reside on the same layer.

Tip: Make sure that you are in Pour Outline mode when attempting to merge or subtract shapes. Use the modeless command PO and press Enter to toggle the setting.