Is every field in the record a duplicate? Or just the two fields you want to index, with some other primary column present?
If all the fields are identical it's easiest to create a second table and copy the rows into it:
insert into newTable select distinct * from oldTable
Otherwise you could just create the second table, make the index unique, and loop through all the rows inserting them. Some of the inserts will fail because of the dupl;icate key, just ignore the error in the loop.