If you want to format the CF card, be sure to copy over any web files or script files you want to keep.
Use your PC and a compact flash card reader to format the card.
Be sure to format the card as FAT32 with Allocation Size of "4096".
The allocation size is important, so be sure to make this selection.
Once completed, Open Winscpript Live and go to tools>"Create Default Flash Card"
Choose your Device type, browse to your CF card location and then select "OK"
If you have an SD or CF card greater than 8GB, see this article for partitioning to a smaller size: