If you mean that you can only restore backup data to the same PS3, I don't think this is the case. You can restore a backup to any PS3 with certain exceptions:
Some types of backed up data can be restored on another PS3™ system. The types of data that can be restored on another system are as follows:
Although I agree that the simplest way to do it is copy all the saves you need by hand to a USB drive.
I don't think recent versions of Windows (not sure about Windows 7 though) will let you format a HDD to FAT32. You'll need third-party software to do it, something like CompuApps Swissknife. If that doesn't work (didn't for me for some reason), you can download Ubuntu and install it on your computer as another OS - it lets you format to any file system you like.
Join our PS3 BF3 server! Search for 'Better than Halo' in the browser and bookmark us, and/or add me on PSN (ThemisB). We play most nights from 8pm GMT. See you on the Battlefield!