Can I protect select files on my external Hard Drive from being formatted?

Seems like you are actually wanting a different answer than your question. You want a utility to erase the empty parts of your drive to protect what was there before?

There are several open source ones out there you can get free. just search on wipe disk utility or erase blank disk areas,...

Just delete everything you want off the disk, then run the utility.

to format a hard drive means to wipe it clean and start over. So you should do something with the data you want to save. Like maybe put them on a USB thumb drive and that way you could transfer them back when you are done with the formatting. otherwise, no you will lose all your information when you format. it's called writing zero's to the hard drive. zero is zero.

You can't do it by formatting. You can just go in and delete everything off the hard drive and leave the stuff you want!