Even though I am not using Linux right now, I think the following links might help you to accomplish what you want:
Converting FAT32 to EXT3 in Ubuntu / any Linux distribution
http://ubuntuforums.org/archive/index.php/t-241169.html
I have read on various forums that you cannot convert from NTFS to EXT3 directly, because of the complex nature of NTFS. But there are some options.
http://www.aeonity.com/frost/convert...ives-ntfs-ext3
http://www.linux-noob.com/forums/ind...?showtopic=636
Gnome Partition Editor for Linux
http://gparted.sourceforge.net/
If someone uses Windows, You can try
Norton PartitionMagic 8.0 which says you can do this:
Supports and converts partitions among FAT, FAT32, NTFS, Ext2, and Ext3 file systems
I am not sure if the above work or not.
But make sure you have made a Backup of the HDD before starting to convert.
Lemme know if any of them helped you.