If the ISO files on your PC are ISO images of Emulator-III cdroms, you can simply do a raw copy of this ISO file to your CF card.
It's like restoring a hard disk. Of course you'll need a CF card reader connected to your PC.
On Windows you can use software like HDD Raw Copy Tool from HDDGuru.
(you can find this freeware here:
http://hddguru.com/software/HDD-Raw-Copy-Tool/)
Simply select the ISO file as SOURCE, then the CF card drive as TARGET and start the copy.
As an alternative on Windows, you can use EMXP (
http://www.emxp.net) to restore these ISO files to a CF card
(but you'll first have to replace the .ISO extension by the .EZ3 extension).
EMXP can also read/write/copy individual Emulator-III banks from/to EIII formatted CF cards.
For OSX I have no idea, but Wolfram seems to have interesting hints !