Are you sure you have two drives? My G53 came with one drive, but it was formatted into two partitions. If you want to format the data drive/partition, go into "Computer" right-click on the drive, and select "Format". Windows will make sure that you really want to do so, then offer you choices in how to format the drive. The default settings are fine, as long as it selects NTFS.
For the OS drive, the process is a little trickier. Get out your recovery DVDs, and boot from them. Windows will offer to reinstall or repair. Format the appropriate partition, and install Windows to that one. You may have to choose advanced options to make sure that it does not do a factory restore.
Still, why do you think you need to reformat? A few fragmented files woll not slow down your computer.