Most likely (depending on your HDD size), it will take some time to format. There is no way to selectively format just portions of you disk. If you erase the disk headers, boot sector, FAT, etc. you may still be able to retrieve the information for a substantial fee from a professional data recovery company. If you do a complete format, the sectors of the disk are completely wiped with all zero's, or one's, I can't remember. If you lose power, just start over; it's cleaner.
The best bet for data integrity is backups.
If you want to wipe you HDD before installing a new OS, for an IDE drive, boot from an MS-Dos disk and run this debug routine. The xxxx:0100 etc. are what you will be displayed. The MOV AX,301 is what you will enter:

-FCS:200 400 0
-ACS:100
xxxx:0100 MOV AX,301
xxxx:0103 MOV BX,200
xxxx:0106 MOV CX,1
xxxx:0109 MOV DX,80
xxxx:010C INT 13
xxxx:010E INT 20
xxxx:0110 <enter>
-G
Program Terminated Normally
-Q