I'm preparing a previously set up SDCard for Installing a CoPiino (Arduino Hat for Raspberry Pi). The problem is that Windows only recognizes the first partition on a SDCard. Here are the steps I took to remove the old Raspberry Pi partitions, and prepare the card for a new Raspian install.
Start a command prompt, and type in DISKPART and press Enter to 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 SD card). You can then type CLEAN (MAKE SURE YOU SELECTED THE PROPER DISK!), 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.
Download SD FORMATTER and format the SDCard.
DOWNLOAD & COPY THE RASPIAN IMAGE
Go to http://www.raspberrypi.org/help/noobs-setup/ and follow the instructions for downloading and copying the image to the SDCard. Then boot the Rasperry Pi, and finish the install normally.