Library dependency woes

One of my Unix workstation is now fucked up due to forced installation of incompatible libraries. I guess I'll have to reformat it in order to start from a clean slate. I'm planning to temporarily transfer my files to my external harddisk, but FreeBSD can't seem to read it although it has been formatted as UFS. I formatted that harddisk on my Mac OS X laptop, thinking that it can be read in FreeBSD, but Mac OS X seems to have a different interpretation of what UFS is. Blah. I guess I need to reformat my external harddisk to FAT32 too. Oh wait. If I format it as FAT32, what would happen with my file permissions? Maybe I'll just use tar or something. Blah, blah, blah.