I've never owned a Zeiss CLSM but I did play around with one a bit.
As I recall all file names were just numbers - there was no provision
for standard DOS file names.  This suggests - but of course doesn't
prove - that on their embedded computer the hard disk wasn't using
a standard DOS file structure.  In that case, if they don't give you
a utility to do a high-level format, you are completely at their mercy!
You could buy an identical 20MB hard disk, but you couldn't format it.
For that reason Andy Cameron's solution sounds like a better bet.
 
                        Guy Cox
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