At Mullone the Spirit Guide who can be found at the very top (north) of Devil’s Crossing main town.
On his interface you left click the skill you wish to remove a point from. It costs to remove each point (25). Your total funds are on the left and you’ll see that figure decrease as you remove skill points.
You can undo all the points you remove by clicking ‘Undo Points’ in the top right of his interface and this will re add the points to all the skills and give you back your money.