This guide works for a Windows computer. Doing the same from a Linux client requires different command, but the steps are the same.
Start a command prompt, and start the DISKPART console. List all of your disks by typing LIST DISK, then select the proper disk with SELECT DISK # (where # is obviously the CF-card). Check with LIST DISK that you selected the correct disk, which after the select has a “*” mark in front of the disk information. You can then type CLEAN, and it will clear the partition table on the card.
To create a primary partition to reuse the space on the card, type CREATE PARTITION PRIMARY. This will then reallocate the previously “cleaned” space.
To format, type FORMAT FS=FAT32 QUICK, and finally, to reassign a drive letter, type ASSIGN.
If you're unable to determine the proper disk, remove the CF-card, run DISKPART and LIST DISK, and then re-run it with the CF-card inserted. The CF-card is just the disk that has been added.
Here is the original article.