Most of the external disk drives that I have had the occasion to take apart have had a standard SATA disk drive inside. If yours is like that, then you should be able to put them in a multi-bay Thunderbolt SATA enclosure without problems.
Note: if your Thunderbolt enclosure has "hardware RAID" capability, you will probably need matched drives for all slots, and may require only certain models of drives (see the enclosure spec sheets for qualified drives).