You will need to place an offsetting order against your current position to settle it. Buy positions will be settled through a sell-back, and sell positions will be settled through a buy-back. Positions will be settled following the FIFO method.
If you have a position, placing an order will make a settlement order.
Otherwise, it will be a new order. When making a settlement order, settlements will be performed in order from the oldest positions. If there is any amount in excess of the amount that can be settled, the difference will become a new order.
Please see bitFlyer Crypto CFD Trading Rules for further details.