Leave the motherboard in the case? Of course you can, just be sure to have everything disconnected from the GPU, there may be a power lead or two depending on the card type. There will be one or two screws attaching the steel bracket at the back of the card (the one where all the ports are) to the PC case. In addition there should be a retention latch securing the card to the motherboard slot, this lil guy will be spring loaded and you'll have to hold it "open" while you remove the card. This latch is part of the slot you are pulling the card from. Also be sure to ground yourself to the PC case, continue doing so from time to time while you work.