in the name box (to the left of the formula bar formula text box) put in something like
1000:65536 <enter>
hit delete
where 1000 marks the first row you believe is empty.
make 65536 to be the last row you want deleted
You can get this number by do F5 then special and choosing last cell and noting the row.
reference entering the row range in the namebox
this will select all the designated rows and then you delete them.
Now save the file. this should cause Excel to revise what it considers to be the last used row.
Do this on every sheet
or you could write a macro to do this - fortunately Debra Dalgleish has already done this:
http://www.contextures.com/xlfaqApp.html#Unused
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Regards,
Tom Ogilvy